void palOptions(struct cart *cart,
struct sqlConnection *conn, void (*addButtons)(),
char *extraVar)
/* output the options dialog (select MAF file, output options */
{
char *database = sqlGetDatabase(conn);
hPrintf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=POST>\n", cgiScriptName());
cartSaveSession(cart);
char *mafTable = outMafTableDrop(cart, conn);
char *numColumns = cartUsualString(cart, hgtaCGINumColumns, "");
printf("<BR><BR><B>Formatting options:</B><BR>\n");
jsMakeTrackingCheckBox(cart, hgtaCGIGeneExons, hgtaJSGeneExons, FALSE);
printf("Separate into exons<BR>");
jsMakeTrackingCheckBox(cart, hgtaCGIGeneNoTrans, hgtaJSGeneNoTrans, FALSE);
printf("Show nucleotides<BR>");
jsMakeTrackingCheckBox(cart, hgtaCGIGeneOutBlank, hgtaJSGeneOutBlank, FALSE);
printf("Output lines with just dashes<BR>");
jsMakeTrackingCheckBox(cart, hgtaCGIOutTable, hgtaJSOutTable, FALSE);
printf("Format output as table ");
jsMakeTrackingCheckBox(cart, hgtaCGITruncHeader, hgtaJSTruncHeader, FALSE);
printf("Truncate headers at ");
cgiMakeTextVar(hgtaCGINumColumns, numColumns, 2);
printf("characters (enter zero for no headers)<BR>");
printf("<BR>");
struct trackDb *maftdb = hTrackDbForTrack(database, mafTable);
/* get maf parent (if any) */
maftdb->parent = hCompositeTrackDbForSubtrack(database,maftdb);
wigMafSpeciesTable(cart, maftdb, mafTable, database);
addButtons();
cartSaveSession(cart);
hPrintf("</FORM>\n");
/* Hidden form - for benefit of javascript. */
{
static char *saveVars[32];
int varCount = ArraySize(curVars);
assert(varCount < (sizeof saveVars / sizeof(char *)));
memcpy(saveVars, curVars, varCount * sizeof(saveVars[0]));
if (extraVar != NULL)
{
assert(varCount + 1 < (sizeof saveVars / sizeof(char *)));
saveVars[varCount] = extraVar;
varCount++;
}
jsCreateHiddenForm(cart, cgiScriptName(), saveVars, varCount);
}
}
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();
}
static void doBigFilterPage(struct sqlConnection *conn, char *db, char *table)
/* Put up filter page on given db.table. */
{
struct joiner *joiner = allJoiner;
struct dbTable *dtList, *dt;
char dbTableBuf[256];
if (strchr(table, '.'))
htmlOpen("Filter on Fields from %s", table);
else
htmlOpen("Filter on Fields from %s.%s", db, table);
jsIncludeFile("jquery.js", NULL);
jsIncludeFile("utils.js", NULL);
commonCssStyles();
hPrintf("<FORM ACTION=\"%s\" METHOD=%s>\n", cgiScriptName(),
cartUsualString(cart, "formMethod", "POST"));
cartSaveSession(cart);
cgiMakeHiddenVar(hgtaDatabase, db);
cgiMakeHiddenVar(hgtaTable, table);
dbOverrideFromTable(dbTableBuf, &db, &table);
filterControlsForTable(db, table);
dtList = extraTableList(filterLinkedTablePrefix);
showLinkedFilters(dtList);
dt = dbTableNew(db, table);
slAddHead(&dtList, dt);
showLinkedTables(joiner, dtList, filterLinkedTablePrefix,
hgtaDoFilterMore, "allow filtering using fields in checked tables");
hPrintf("</FORM>\n");
cgiDown(0.9);
htmlClose();
}
void doUploadIdentifiers(struct sqlConnection *conn)
/* Respond to upload identifiers button. */
{
struct hTableInfo *hti = maybeGetHti(database, curTable, conn);
char *idField = getIdField(database, curTrack, curTable, hti);
htmlOpen("Upload Identifiers for %s", curTableLabel());
if (idField == NULL)
errAbort("Sorry, I can't tell which field of table %s to treat as the "
"identifier field.", curTable);
hPrintf("<FORM ACTION=\"%s\" METHOD=POST ENCTYPE=\"multipart/form-data\">\n",
getScriptName());
cartSaveSession(cart);
hPrintf("Please enter the name of a file from your computer that contains a ");
hPrintf("space, tab, or ");
hPrintf("line separated list of the items you want to include.\n");
explainIdentifiers(database, conn, idField);
hPrintf("<BR>\n");
hPrintf("<INPUT TYPE=FILE NAME=\"%s\"> ", hgtaPastedIdentifiers);
hPrintf("<BR>\n");
cgiMakeButton(hgtaDoPastedIdentifiers, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>");
cgiDown(0.9);
htmlClose();
}
void userSettingsLoadForm(struct userSettings *us)
/* Put up controls that let user name and save the current
* set. */
{
struct hashEl *list = cartFindPrefix(us->cart, us->savePrefix);
/* Start form/save session/print title. */
hPrintf("<FORM ACTION=\"../cgi-bin/hgNear\" NAME=\"usForm\" METHOD=GET>\n");
cartSaveSession(us->cart);
hPrintf("<H2>Load %s</H2>\n", us->formTitle);
hPrintf("<TABLE><TR><TD>\n");
hPrintf("<SELECT NAME=\"%s\" SIZE=%d>",
us->nameVar, slCount(list));
printLabelList(us, list);
hPrintf("</SELECT>");
hPrintf("</TD><TD>");
cgiMakeButton(us->formVar, "load");
hPrintf(" ");
cgiMakeButton(us->formVar, "cancel");
hPrintf("</TD></TR></TABLE>");
/* Cleanup. */
hPrintf("</FORM>\n");
slFreeList(&list);
}
void doSetUserRegions(struct sqlConnection *conn)
/* Respond to set regions button. */
{
char *oldPasted = cartUsualString(cart, hgtaEnteredUserRegions, "");
char *db = cartOptionalString(cart, hgtaUserRegionsDb);
if (db && !sameString(db, database))
oldPasted = "";
htmlOpen("Enter region definition\n");
hPrintf("<FORM ACTION=\"%s\" METHOD=POST "
" ENCTYPE=\"multipart/form-data\" NAME=\"mainForm\">\n", getScriptName());
cartSaveSession(cart);
hPrintf("<TABLE><TR><TD ALIGN=LEFT>\n");
hPrintf("Paste regions:");
hPrintf("</TD><TD ALIGN=RIGHT>");
hPrintf("Or upload file: <INPUT TYPE=FILE NAME=\"%s\"> <BR>\n",
hgtaEnteredUserRegionFile);
hPrintf("</TD></TR><TR><TD COLSPAN=2 ALIGN=LEFT>\n");
cgiMakeTextArea(hgtaEnteredUserRegions, oldPasted, 10, 70);
hPrintf("</TD></TR><TR><TD COLSPAN=2 ALIGN=LEFT>\n");
cgiMakeButton(hgtaDoSubmitUserRegions, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoClearSetUserRegionsText, "clear");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</TD></TR></TABLE>");
hPrintf("</FORM><BR>\n");
webIncludeHelpFile("hgTbUserRegionsHelp", FALSE);
htmlClose();
}
void doMainDisplay(struct sqlConnection *conn,
struct column *colList, struct subjInfo *subjList)
/* Put up the main gene sorter display - a control panel followed by
* a big table. */
{
char buf[128];
safef(buf, sizeof(buf), "GSID %s Table View", genome);
hPrintf("<FORM ACTION=\"../cgi-bin/gsidTable\" NAME=\"mainForm\" METHOD=GET>\n");
hotLinks();
cartSaveSession(cart);
printf("<font size=5><B>Table View</B></font>");
mainControlPanel();
if (subjList != NULL)
{
printf("Use the \"configure\" button above to access additional data fields,");
printf(" including infection date details, sequencing and ART date information,");
printf(" and immunogenicity data.");
bigTable(conn, colList,subjList);
}
printf("<br>* Estimated Study Day of Infection (ESDI), ");
printf("click <a href=\"http://www.gsid.org/downloads/methods_and_conventions.pdf\" target=_blank> here </a>");
printf(" for further explanation.\n");
printf("<br>* Days After Estimated Infection (DAEI), ");
printf("click <a href=\"http://www.gsid.org/downloads/methods_and_conventions.pdf\" target=_blank> here </a>");
printf(" for further explanation.\n");
hPrintf("</FORM>\n");
}
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 doBigSelectPage(char *db, char *table)
/* Put up big field selection page. Assumes html page open already*/
{
struct joiner *joiner = allJoiner;
struct dbTable *dtList, *dt;
char dbTableBuf[256];
cartSetString(cart, hgtaFieldSelectTable, getDbTable(db, table));
if (strchr(table, '.'))
htmlOpen("Select Fields from %s", table);
else
htmlOpen("Select Fields from %s.%s", db, table);
hPrintf("<FORM NAME=\"mainForm\" ACTION=\"%s\" METHOD=%s>\n", cgiScriptName(),
cartUsualString(cart, "formMethod", "POST"));
cartSaveSession(cart);
cgiMakeHiddenVar(hgtaDatabase, db);
cgiMakeHiddenVar(hgtaTable, table);
dbOverrideFromTable(dbTableBuf, &db, &table);
showTableFields(db, table, TRUE);
dtList = extraTableList(selFieldLinkedTablePrefix());
showLinkedFields(dtList);
dt = dbTableNew(db, table);
slAddHead(&dtList, dt);
showLinkedTables(joiner, dtList, selFieldLinkedTablePrefix(),
hgtaDoSelectFieldsMore, "allow selection from checked tables");
/* clean up. */
hPrintf("</FORM>");
cgiDown(0.9);
htmlClose();
joinerFree(&joiner);
}
void doControls(struct sqlConnection *conn)
/* Put up controls pane. */
{
char *listSpec = cartUsualString(cart, hgpListSpec, "");
htmlSetBgColor(0xD0FFE0);
// resource file link wrapped in html
char * link = webTimeStampedLinkToResourceOnFirstCall("HGStyle.css",TRUE);
if (link)
htmlSetStyle(link);
htmStart(stdout, "do controls");
printf("<FORM ACTION=\"%s\" NAME=\"mainForm\" target=\"_parent\" METHOD=GET>\n",
hgVisiGeneCgiName());
cartSaveSession(cart);
printf("<TABLE WIDTH=100%%><TR>");
printf("<TD WIDTH=230 bgcolor=\"#"HG_COL_HOTLINKS"\">");
printf(" <B><A HREF=\"../index.html\" target=\"_parent\" class=\"topbar\">UCSC</A> ");
printf(" <A HREF=\"%s?%s=\" target=\"_parent\" class=\"topbar\">VisiGene</A></B> ",
hgVisiGeneCgiName(), hgpListSpec);
printf("</TD>");
printf("<TD>");
printf(" ");
cgiMakeTextVar(hgpListSpec, listSpec, 16);
cgiMakeButton(hgpDoSearch, "search");
printf("</TD>");
#ifdef SOON
printf("<TD>");
cgiMakeButton(hgpDoConfig, "configure");
printf("</TD>");
#endif /* SOON */
printf("<TD>");
printf("Zoom: ");
printf(
"<INPUT TYPE=SUBMIT NAME=\"hgp_zmOut\" VALUE=\" out \""
" onclick=\"parent.image.bigImg.zoomer('out');return false;\"> "
"<INPUT TYPE=SUBMIT NAME=\"hgp_zmIn\" VALUE=\" in \""
" onclick=\"parent.image.bigImg.zoomer('in');return false;\"> "
"<INPUT TYPE=SUBMIT NAME=\"hgp_zmFull\" VALUE=\" full \""
" onclick=\"parent.image.bigImg.zoomer('full');return false;\"> "
"<INPUT TYPE=SUBMIT NAME=\"hgp_zmFit\" VALUE=\" fit \""
" onclick=\"parent.image.bigImg.zoomer('fit');return false;\"> "
"\n");
printf("</TD>");
printf("<TD ALIGN=Right>");
printf("<A HREF=\"../goldenPath/help/hgTracksHelp.html#VisiGeneHelp\" target=_parent>");
printf("Help");
printf("</A> ");
printf("</TD>");
printf("</TR></TABLE>");
printf("</FORM>\n");
htmlEnd();
}
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>");
}
void jsCreateHiddenForm(struct cart *cart, char *scriptName,
char **vars, int varCount)
/* Create a hidden form with the given variables */
{
int i;
hPrintf(
"<FORM ACTION=\"%s\" "
"METHOD=\"GET\" NAME=\"hiddenForm\">\n", scriptName);
cartSaveSession(cart);
for (i=0; i<varCount; ++i)
hPrintf("<input type=\"hidden\" name=\"%s\" value=\"\">\n", vars[i]);
puts("</FORM>");
}
static void genePredOptions(struct trackDb *track, char *type,
struct sqlConnection *conn)
/* Put up sequence type options for gene prediction tracks. */
{
char *predType = cartUsualString(cart, hgtaGeneSeqType, genePredMenu[0]);
char *dupType = cloneString(type);
char *typeWords[3];
int typeWordCount, typeIx;
/* Type field has 1-3 words which are in order:
* genePred pepTable mrnaTable */
typeWordCount = chopLine(dupType, typeWords);
/* TypeIx will be 0 (genomic) 1 (protein) 2(mrna). */
typeIx = stringArrayIx(predType, genePredMenu, typeWordCount);
if (typeIx < 0)
predType = genePredMenu[0];
htmlOpen("Select sequence type for %s", track->shortLabel);
hPrintf("<FORM ACTION=\"%s\" METHOD=GET>\n", getScriptName());
cartSaveSession(cart);
if (isRefGeneTrack(track->table))
{
/* RefGene covers all 3 types, but in it's own way. */
for (typeIx = 0; typeIx < 3; ++typeIx)
{
genePredTypeButton(genePredMenu[typeIx], predType);
hPrintf(" %s<BR>\n", genePredMenu[typeIx]);
}
}
else
{
/* Otherwise we always have genomic, and we have
* peptide/mrna only if there are corresponding table
* in the type field. */
for (typeIx = 0; typeIx < typeWordCount; ++typeIx)
{
if (typeIx == 0 || sqlTableExists(conn, typeWords[typeIx]))
{
genePredTypeButton(genePredMenu[typeIx], predType);
hPrintf(" %s<BR>\n", genePredMenu[typeIx]);
}
}
}
cgiMakeButton(hgtaDoGenePredSequence, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>\n");
cgiDown(0.9);
htmlClose();
freez(&dupType);
}
void doConfigure(struct sqlConnection *conn, struct column *colList) //, char *bumpVar)
/* Generate configuration page. */
{
//if (bumpVar)
// bumpColList(bumpVar, &colList);
hPrintf("<FORM ACTION=\"../cgi-bin/gisaidTable\" METHOD=POST>\n");
//makeTitle("Configure Table View", "gisaidTableHelp.html#Configure");
hotLinks();
configControlPanel();
cartSaveSession(cart);
configTable(colList, conn);
hPrintf("</FORM>");
}
void doGetSeqPage(struct sqlConnection *conn, struct column *colList)
/* Put up the get sequence page asking how to get sequence. */
{
hPrintf("<H2>Get Sequence</H2>");
hPrintf("<FORM ACTION=\"../cgi-bin/gisaidTable\" METHOD=GET>\n");
cartSaveSession(cart);
hPrintf("Select sequence type:<BR>\n");
howRadioButton("protein");
hPrintf("Protein<BR>\n");
howRadioButton("genomic");
hPrintf("Genomic<BR>\n");
cgiMakeButton(getSeqVarName, "get sequence");
hPrintf("</FORM>\n");
}
void doMainDisplay(struct sqlConnection *conn,
struct column *colList, struct subjInfo *subjList)
/* Put up the main gene sorter display - a control panel followed by
* a big table. */
{
char buf[128];
safef(buf, sizeof(buf), "GISAID %s Table View", genome);
hPrintf("<FORM ACTION=\"../cgi-bin/gisaidTable\" NAME=\"mainForm\" METHOD=GET>\n");
hotLinks();
cartSaveSession(cart);
printf("<font size=5><B>Table View</B></font>");
mainControlPanel();
if (subjList != NULL)
bigTable(conn, colList,subjList);
hPrintf("</FORM>\n");
}
void userSettingsSaveForm(struct userSettings *us)
/* Put up controls that let user name and save the current
* set. */
{
char buf[1024];
struct hashEl *list = cartFindPrefix(us->cart, us->savePrefix);
safef(buf, sizeof(buf), "Save %s", us->formTitle);
makeTitle(buf, NULL);
/* Start form/save session/print title. */
hPrintf("<FORM ACTION=\"../cgi-bin/hgNear\" NAME=\"usForm\" METHOD=GET>\n");
cartSaveSession(us->cart);
/* Put up controls that are always there. */
hPrintf("Please name this setup:\n");
cartMakeTextVar(us->cart, us->nameVar, "", 16);
hPrintf(" ");
cgiMakeButton(us->formVar, "save");
hPrintf(" ");
cgiMakeButton(us->formVar, "cancel");
/* Put up additional controls if have saved settings already. */
if (list != NULL)
{
struct dyString *js = newDyString(0);
htmlHorizontalLine();
slSort(&list, hashElCmp);
hPrintf("Existing Setups:");
dyStringPrintf(js, "document.usForm.%s.value=", us->nameVar);
dyStringPrintf(js, "document.usForm.%s.options", us->listDisplayVar);
dyStringPrintf(js, "[document.usForm.%s.selectedIndex].value;", us->listDisplayVar);
hPrintf("<SELECT NAME=\"%s\" SIZE=%d onchange=\"%s\">",
us->listDisplayVar, slCount(list), js->string);
printLabelList(us, list);
hPrintf("</SELECT>\n");
cgiMakeButton(us->formVar, "delete existing setup");
}
/* Cleanup. */
hPrintf("</FORM>\n");
slFreeList(&list);
}
static void vcfRecordDetails(struct trackDb *tdb, struct vcfRecord *rec)
/* Display the contents of a single line of VCF, assumed to be from seqName
* (using seqName instead of rec->chrom because rec->chrom might lack "chr"). */
{
printf("<B>Name:</B> %s<BR>\n", rec->name);
// Since these are variants, if it looks like a dbSNP or dbVar ID, provide a link:
if (regexMatch(rec->name, "^rs[0-9]+$"))
{
printf("<B>dbSNP:</B> ");
printDbSnpRsUrl(rec->name, "%s", rec->name);
puts("<BR>");
}
else if (regexMatch(rec->name, "^[en]ss?v[0-9]+$"))
{
printf("<B>dbVar:</B> ");
printf("<A HREF=\"http://www.ncbi.nlm.nih.gov/dbvar/variants/%s/\" "
"TARGET=_BLANK>%s</A><BR>\n", rec->name, rec->name);
}
printCustomUrl(tdb, rec->name, TRUE);
boolean hapClustEnabled = cartOrTdbBoolean(cart, tdb, VCF_HAP_ENABLED_VAR, TRUE);
if (hapClustEnabled)
{
static char *formName = "vcfCfgHapCenter";
printf("<FORM NAME=\"%s\" ACTION=\"%s\">\n", formName, hgTracksName());
cartSaveSession(cart);
vcfCfgHaplotypeCenter(cart, tdb, tdb->track, FALSE, rec->file, rec->name,
seqName, rec->chromStart, formName);
printf("</FORM>\n");
}
char leftBase = rec->alleles[0][0];
unsigned int vcfStart = vcfRecordTrimIndelLeftBase(rec);
boolean showLeftBase = (rec->chromStart == vcfStart+1);
(void)vcfRecordTrimAllelesRight(rec);
char *displayAls[rec->alleleCount];
makeDisplayAlleles(rec, showLeftBase, leftBase, 20, TRUE, FALSE, displayAls);
printPosOnChrom(seqName, rec->chromStart, rec->chromEnd, NULL, FALSE, rec->name);
printf("<B>Reference allele:</B> %s<BR>\n", displayAls[0]);
vcfAltAlleleDetails(rec, displayAls);
vcfQualDetails(rec);
vcfFilterDetails(rec);
vcfInfoDetails(rec);
pgSnpCodingDetail(rec);
makeDisplayAlleles(rec, showLeftBase, leftBase, 5, FALSE, TRUE, displayAls);
vcfGenotypesDetails(rec, tdb, displayAls);
}
void doAdvFilterKeyPaste(struct sqlConnection *conn, struct column *colList,
struct column *col)
/* Handle upload keyword list button press in advanced filter form. */
{
char *varName = NULL;
char buf[1024];
cartRemovePrefix(cart, keyWordPastePrefix);
safef(buf, sizeof(buf), "Paste List : %s - %s", col->shortLabel, col->longLabel);
makeTitle(buf, NULL);
hPrintf("<FORM ACTION=\"../cgi-bin/hgNear\" METHOD=POST>\n");
cartSaveSession(cart);
hPrintf("Paste in a list of items to match. ");
cgiMakeButton("submit", "submit");
hPrintf("<BR>\n");
varName = colVarName(col, keyWordPastedPrefix);
cgiMakeTextArea(varName, "", 10, 60);
hPrintf("</FORM>");
}
void doAdvFilterKeyUpload(struct sqlConnection *conn, struct column *colList,
struct column *col)
/* Handle upload keyword list button press in advanced filter form. */
{
char *varName = NULL;
char buf[1024];
cartRemovePrefix(cart, keyWordUploadPrefix);
safef(buf, sizeof(buf), "Upload List : %s - %s", col->shortLabel, col->longLabel);
makeTitle(buf, NULL);
hPrintf("<FORM ACTION=\"../cgi-bin/hgNear\" METHOD=POST ENCTYPE=\"multipart/form-data\">\n");
cartSaveSession(cart);
hPrintf("Enter the name of a file from your computer that contains a list");
hPrintf("of items separated by a space, tab or line.<BR>");
varName = colVarName(col, keyWordPastedPrefix);
hPrintf("<INPUT TYPE=FILE NAME=\"%s\"> ", varName);
cgiMakeButton("submit", "submit");
hPrintf("</FORM>");
}
void correlatePage(struct sqlConnection *conn)
/* Put up correlation page. */
{
cartWebStart(cart, database, "Correlations of all pairs of graphs");
hPrintf("<FORM ACTION=\"../cgi-bin/hgGenome\" METHOD=GET>\n");
cartSaveSession(cart);
struct slRef *ggRefList = ggAllVisible(conn);
struct slRef *aRef, *bRef;
hPrintf("<TABLE><TR><TD>");
webPrintLinkTableStart();
webPrintLabelCell("Graph A");
webPrintLabelCell("Graph B");
webPrintLabelCell("R");
webPrintLabelCell("R-Squared");
for (aRef = ggRefList; aRef != NULL; aRef = aRef->next)
{
for (bRef = aRef->next; bRef != NULL; bRef = bRef->next)
{
hPrintf("</TR><TR>");
correlateGraphs(aRef->val, bRef->val);
}
}
webPrintLinkTableEnd();
hPrintf("</TD><TD>");
hPrintf("<CENTER>");
cgiMakeButton("submit", "return to graphs");
hPrintf("</CENTER>");
hPrintf("</TD></TR></TABLE>");
hPrintf("<P>R, also known as Pearson's correlation coefficient, is a measure ");
hPrintf("of the extent that two graphs move together. The value of R ranges ");
hPrintf("between -1 and 1. A positive R indicates that the graphs tend to ");
hPrintf("move in the same direction, while a negative R indicates that they ");
hPrintf("tend to move in opposite directions.</P>\n");
hPrintf("<P>R-Squared (which is indeed just R*R) measures how much of the ");
hPrintf("variation in one graph can be explained by a linear dependence on ");
hPrintf("the other graph. R-Squared ranges between 0 when the two graphs are ");
hPrintf("independent to 1 when the graphs are completely dependent.</P>");
hPrintf("</FORM>");
cartWebEnd();
}
void doPasteIdentifiers(struct sqlConnection *conn)
/* Respond to paste identifiers button. */
{
struct sqlConnection *alternateConn = conn;
char *actualDb = database;
if (sameWord(curTable, WIKI_TRACK_TABLE))
{
alternateConn = wikiConnect();
actualDb = wikiDbName();
}
char *oldPasted = forCurTable() ?
cartUsualString(cart, hgtaPastedIdentifiers, "") : "";
struct hTableInfo *hti = maybeGetHti(actualDb, curTable, conn);
char *idField = getIdField(actualDb, curTrack, curTable, hti);
htmlOpen("Paste In Identifiers for %s", curTableLabel());
if (idField == NULL)
errAbort("Sorry, I can't tell which field of table %s to treat as the "
"identifier field.", curTable);
hPrintf("<FORM ACTION=\"%s\" METHOD=%s>\n", getScriptName(),
cartUsualString(cart, "formMethod", "POST"));
cartSaveSession(cart);
hPrintf("Please paste in the identifiers you want to include.\n");
if (sqlDatabaseExists("hgTemp"))
explainIdentifiers(actualDb, alternateConn, idField);
else
warn("No hgTemp database found for temporary tables.<br>Please src/product/README.mysql.setup for more information.");
hPrintf("<BR>\n");
cgiMakeTextArea(hgtaPastedIdentifiers, oldPasted, 10, 70);
hPrintf("<BR>\n");
cgiMakeButton(hgtaDoPastedIdentifiers, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoClearPasteIdentifierText, "clear");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>");
cgiDown(0.9);
htmlClose();
if (sameWord(curTable, WIKI_TRACK_TABLE))
wikiDisconnect(&alternateConn);
}
void doTrackForm(char *psOutput, char *psOutput2)
/* Make the tracks display form */
{
if (psOutput != NULL)
{
suppressHtml = TRUE;
hideControls = TRUE;
}
/* Tell browser where to go when they click on image. */
hPrintf("<FORM ACTION=\"%s\" NAME=\"TrackForm\" METHOD=POST>\n\n", "../cgi-bin/pbGlobal");
cartSaveSession(cart);
hPrintf("<TABLE WIDTH=\"100%%\" BGCOLOR=\"#"HG_COL_HOTLINKS"\" BORDER=\"0\" CELLSPACING=\"0\" CELLPADDING=\"2\"><TR>\n");
hPrintf("<TD ALIGN=LEFT><A HREF=\"../index.html\">%s</A></TD>", wrapWhiteFont("Home"));
hPrintf("<TD style='text-align:center; color:#FFFFFF; font-size:medium;'>%s</TD>",
"UCSC Proteome Browser");
hPrintf("<TD ALIGN=CENTER><A HREF=\"../cgi-bin/pbGlobal?%s=%u&pbt.psOutput=on\">%s</A></TD>\n",
cartSessionVarName(), cartSessionId(cart), wrapWhiteFont("PDF/PS"));
hPrintf("<TD ALIGN=CENTER><A HREF=\"../cgi-bin/pbGateway\">%s</A></TD>", wrapWhiteFont("New Query"));
if (proteinInSupportedGenome)
{
hPrintf("<TD ALIGN=Right><A HREF=\"../goldenPath/help/pbTracksHelpFiles/pbTracksHelp.shtml\" TARGET=_blank>%s</A></TD>",
wrapWhiteFont("Help"));
}
else
{
hPrintf("<TD ALIGN=Right><A HREF=\"../goldenPath/help/pbTracksHelpFiles/pbTracksHelp.shtml\" TARGET=_blank>%s</A></TD>",
wrapWhiteFont("Help"));
}
hPrintf("</TR></TABLE>");
fflush(stdout);
/* Make clickable image and map. */
makeActiveImagePB(psOutput, psOutput2);
if (psOutput == NULL) hPrintf("</FORM>");
}
void configureOnePage()
/* Put up configuration for one graph. */
{
/* Figure out which graph we're configuring. */
char *graphName = cartString(cart, "g");
struct genoGraph *gg = hashFindVal(ggHash, graphName);
if (gg == NULL)
{
/* Warn/return rather than abort if have problems, so that
* cartRemovePrefix(hggDo) is executed to keep us from error
* loop forever... */
warn("Graph %s not found", graphName);
return;
}
/* Put up web page with controls */
cartWebStart(cart, database, "Configure %s", gg->shortLabel);
hPrintf("<FORM ACTION=\"../cgi-bin/hgGenome\" METHOD=GET>\n");
cartSaveSession(cart);
cgiMakeHiddenVar(hggConfigure, "on");
struct chromGraphSettings *cgs = gg->settings;
char varName[chromGraphVarNameMaxSize];
chromGraphVarName(gg->name, "minVal", varName);
hPrintf("display min value: ");
cartMakeIntVar(cart, varName, cgs->minVal, 5);
chromGraphVarName(gg->name, "maxVal", varName);
hPrintf(" max value: ");
cartMakeIntVar(cart, varName, cgs->maxVal, 5);
hPrintf("<BR>\n");
hPrintf("draw connecting lines between markers separated by up to ");
chromGraphVarName(gg->name, "maxGapToFill", varName);
cartMakeIntVar(cart, varName, cgs->maxGapToFill, 8);
hPrintf(" bases.");
hPrintf("<BR>\n");
cgiMakeButton("submit", "submit");
hPrintf("</FORM>\n");
cartWebEnd();
}
void submitUpload(struct sqlConnection *conn)
/* Called when they've submitted from uploads page */
{
char *urlText = cartUsualString(cart, hggUploadUrl, NULL);
char *fileText = cartUsualString(cart, hggUploadFile, NULL);
char *rawText = urlText;
if (isNotEmpty(fileText))
rawText = fileText;
int rawTextSize = strlen(rawText);
struct errCatch *errCatch = errCatchNew();
cartWebStart(cart, database, "Data Upload Complete (%d bytes)", rawTextSize);
hPrintf("<FORM ACTION=\"../cgi-bin/hgGenome\">");
cartSaveSession(cart);
if (errCatchStart(errCatch))
trySubmitUpload(conn, rawText);
errCatchFinish(&errCatch);
cartRemove(cart, hggUploadFile);
hPrintf("<CENTER>");
cgiMakeButton("submit", "OK");
hPrintf("</CENTER>");
hPrintf("</FORM>");
cartWebEnd();
}
void doSubtrackMergeMore(struct sqlConnection *conn)
/* Respond to subtrack merge create/edit button */
{
char *dbTable = getDbTable(database, curTable);
htmlOpen("Merge subtracks of %s (%s)",
curTrack->table, curTrack->longLabel);
hPrintf("<FORM ACTION=\"../cgi-bin/hgTables\" NAME=\"mainForm\" METHOD=%s>\n",
cartUsualString(cart, "formMethod", "POST"));
cartSaveSession(cart);
/* Currently selected subtrack table will be the primary subtrack in the
* merge. */
cgiMakeHiddenVar(hgtaNextSubtrackMergePrimary, dbTable);
hPrintf("<H3>Select a subset of subtracks to merge:</H3>\n");
hCompositeUi(database, cart, curTrack, curTable, hgtaDoSubtrackMergePage, "mainForm",
fullTrackHash);
hPrintf("<H3>Select a merge operation:</H3>\n");
struct trackDb *primary = subTdbFind(curTrack,curTable);
if (isWiggle(database, curTable) || isBedGraph(curTable) || isBigWigTable(curTable))
showWiggleMergeOptions(primary->longLabel);
else
showBedMergeOptions();
hPrintf("If a filter is specified on the main Table Browser page, it will "
"be applied only to %s, not to any other selected subtrack. ",
primary->longLabel);
hPrintf("If an intersection is specified on the main page, it will be applied "
"to the result of this merge.<P>\n");
hPrintf("<P>\n");
cgiMakeButton(hgtaDoSubtrackMergeSubmit, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>\n");
htmlClose();
}
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 askForSeq(char *organism, char *db)
/* Put up a little form that asks for sequence.
* Call self.... */
{
struct serverTable *serve = NULL;
/* JavaScript to update form when org changes */
char *onChangeText = "onchange=\""
"document.mainForm.changeInfo.value='orgChange';"
"document.mainForm.submit();\"";
char *userSeq = NULL;
serve = findServer(db, FALSE);
printf(
"<FORM ACTION=\"../cgi-bin/hgBlat\" METHOD=\"POST\" ENCTYPE=\"multipart/form-data\" NAME=\"mainForm\">\n"
"<H2>BLAT Search Genome</H2>\n");
cartSaveSession(cart);
puts("\n");
puts("<INPUT TYPE=HIDDEN NAME=changeInfo VALUE=\"\">\n");
puts("<TABLE BORDER=0 WIDTH=80>\n<TR>\n");
printf("<TD ALIGN=CENTER>Genome:</TD>");
printf("<TD ALIGN=CENTER>Assembly:</TD>");
printf("<TD ALIGN=CENTER>Query type:</TD>");
printf("<TD ALIGN=CENTER>Sort output:</TD>");
printf("<TD ALIGN=CENTER>Output type:</TD>");
printf("<TD ALIGN=CENTER> </TD>");
printf("</TR>\n<TR>\n");
printf("<TD ALIGN=CENTER>\n");
printBlatGenomeListHtml(db, onChangeText);
printf("</TD>\n");
printf("<TD ALIGN=CENTER>\n");
printBlatAssemblyListHtml(db);
printf("</TD>\n");
printf("<TD ALIGN=CENTER>\n");
cgiMakeDropList("type", typeList, ArraySize(typeList), NULL);
printf("</TD>\n");
printf("<TD ALIGN=CENTER>\n");
cgiMakeDropList("sort", sortList, ArraySize(sortList), cartOptionalString(cart, "sort"));
printf("</TD>\n");
printf("<TD ALIGN=CENTER>\n");
cgiMakeDropList("output", outputList, ArraySize(outputList), cartOptionalString(cart, "output"));
printf("</TD>\n");
printf("</TR>\n<TR>\n");
userSeq = cartUsualString(cart, "userSeq", "");
printf("<TD COLSPAN=5 ALIGN=CENTER>\n");
printf("<TEXTAREA NAME=userSeq ROWS=14 COLS=80>%s</TEXTAREA>\n", userSeq);
printf("</TD>\n");
printf("</TR>\n<TR>\n");
printf("<TD COLSPAN=5 ALIGN=CENTER>\n");
printf("<INPUT TYPE=SUBMIT NAME=Submit VALUE=submit>\n");
printf("<INPUT TYPE=SUBMIT NAME=Lucky VALUE=\"I'm feeling lucky\">\n");
printf("<INPUT TYPE=SUBMIT NAME=Clear VALUE=clear>\n");
printf("</TD>\n");
printf("</TR>\n<TR>\n");
puts("<TD COLSPAN=5 WIDTH=\"100%\">\n"
"Paste in a query sequence to find its location in the\n"
"the genome. Multiple sequences may be searched \n"
"if separated by lines starting with '>' followed by the sequence name.\n"
"</TD>\n"
"</TR>\n"
);
puts("<TR><TD COLSPAN=5 WIDTH=\"100%\">\n");
puts("<BR><B>File Upload:</B> ");
puts("Rather than pasting a sequence, you can choose to upload a text file containing "
"the sequence.<BR>");
puts("Upload sequence: <INPUT TYPE=FILE NAME=\"seqFile\">");
puts(" <INPUT TYPE=SUBMIT Name=Submit VALUE=\"submit file\"><P>\n");
printf("%s",
"<P>Only DNA sequences of 25,000 or fewer bases and protein or translated \n"
"sequence of 10000 or fewer letters will be processed. Up to 25 sequences\n"
"can be submitted at the same time. The total limit for multiple sequence\n"
"submissions is 50,000 bases or 25,000 letters.\n</P>");
if (hgPcrOk(db))
printf("<P>For locating PCR primers, use <A HREF=\"../cgi-bin/hgPcr?db=%s\">In-Silico PCR</A>"
" for best results instead of BLAT.</P>", db);
puts("</TD></TR></TABLE>\n");
printf("</FORM>\n");
webNewSection("About BLAT");
printf(
"<P>BLAT on DNA is designed to\n"
"quickly find sequences of 95%% and greater similarity of length 25 bases or\n"
"more. It may miss more divergent or shorter sequence alignments. It will find\n"
"perfect sequence matches of 20 bases.\n"
"BLAT on proteins finds sequences of 80%% and greater similarity of length 20 amino\n"
"acids or more. In practice DNA BLAT works well on primates, and protein\n"
"blat on land vertebrates."
);
printf("%s",
"\n</P><P>BLAT is not BLAST. DNA BLAT works by keeping an index of the entire genome\n"
"in memory. The index consists of all overlapping 11-mers stepping by 5 except for\n"
"those heavily involved in repeats. The index takes up about\n"
"2 gigabytes of RAM. RAM can be further reduced to less than 1 GB by increasing step size to 11.\n"
"The genome itself is not kept in memory, allowing\n"
"BLAT to deliver high performance on a reasonably priced Linux box.\n"
"The index is used to find areas of probable homology, which are then\n"
"loaded into memory for a detailed alignment. Protein BLAT works in a similar\n"
"manner, except with 4-mers rather than 11-mers. The protein index takes a little\n"
"more than 2 gigabytes.</P>\n"
"<P>BLAT was written by <A HREF=\"mailto:[email protected]\">Jim Kent</A>.\n"
"Like most of Jim's software, interactive use on this web server is free to all.\n"
"Sources and executables to run batch jobs on your own server are available free\n"
"for academic, personal, and non-profit purposes. Non-exclusive commercial\n"
"licenses are also available. See the \n"
"<A HREF=\"http://www.kentinformatics.com\" TARGET=_blank>Kent Informatics</A>\n"
"website for details.</P>\n"
"\n"
"<P>For more information on the graphical version of BLAT, click the Help \n"
"button on the top menu bar");
if (hIsGsidServer())
printf(". </P> \n");
else
printf(" or see the Genome Browser <A HREF=\"../FAQ/FAQblat.html\">FAQ</A>. </P> \n");
}
void doSearchTracks(struct group *groupList)
{
if (!advancedJavascriptFeaturesEnabled(cart))
{
warn("Requires advanced javascript features.");
return;
}
struct group *group;
char *groups[128];
char *labels[128];
int numGroups = 1;
groups[0] = ANYLABEL;
labels[0] = ANYLABEL;
char *currentTab = cartUsualString(cart, TRACK_SEARCH_CURRENT_TAB, "simpleTab");
char *nameSearch = cartOptionalString(cart, TRACK_SEARCH_ON_NAME);
#ifdef TRACK_SEARCH_ON_TYPE
char *typeSearch = cartOptionalString(cart, TRACK_SEARCH_ON_TYPE);
#else///ifndef TRACK_SEARCH_ON_TYPE
char *typeSearch = NULL;
#endif///def TRACK_SEARCH_ON_TYPE
char *descSearch;
char *groupSearch = cartOptionalString(cart, TRACK_SEARCH_ON_GROUP);
boolean doSearch = sameString(cartOptionalString(cart, TRACK_SEARCH), "Search") || cartUsualInt(cart, TRACK_SEARCH_PAGER, -1) >= 0;
struct sqlConnection *conn = hAllocConn(database);
boolean metaDbExists = sqlTableExists(conn, "metaDb");
int numMetadataSelects, tracksFound = 0;
int numMetadataNonEmpty = 0;
char **mdbVar = NULL;
char **mdbVal = NULL;
#ifdef ONE_FUNC
struct hash *parents = newHash(4);
#endif///def ONE_FUNC
boolean simpleSearch;
struct trix *trix;
char trixFile[HDB_MAX_PATH_STRING];
char **descWords = NULL;
int descWordCount = 0;
boolean searchTermsExist = FALSE;
int cols;
char buf[512];
if(sameString(currentTab, "simpleTab"))
{
descSearch = cartOptionalString(cart, TRACK_SEARCH_SIMPLE);
simpleSearch = TRUE;
freez(&nameSearch);
#ifdef TRACK_SEARCH_ON_TYPE
freez(&typeSearch);
#endif///def TRACK_SEARCH_ON_TYPE
freez(&groupSearch);
}
else
{
descSearch = cartOptionalString(cart, TRACK_SEARCH_ON_DESCR);
simpleSearch = FALSE;
}
if(descSearch)
stripChar(descSearch, '"');
trackList = getTrackList(&groupList, -2); // global
makeGlobalTrackHash(trackList);
// NOTE: This is necessary when container cfg by '*' results in vis changes
// This will handle composite/view override when subtrack specific vis exists, AND superTrack reshaping.
parentChildCartCleanup(trackList,cart,oldVars); // Subtrack settings must be removed when composite/view settings are updated
getSearchTrixFile(database, trixFile, sizeof(trixFile));
trix = trixOpen(trixFile);
slSort(&groupList, gCmpGroup);
for (group = groupList; group != NULL; group = group->next)
{
groupTrackListAddSuper(cart, group);
if (group->trackList != NULL)
{
groups[numGroups] = cloneString(group->name);
labels[numGroups] = cloneString(group->label);
numGroups++;
if (numGroups >= ArraySize(groups))
internalErr();
}
}
safef(buf, sizeof(buf),"Search for Tracks in the %s %s Assembly", organism, hFreezeFromDb(database));
webStartWrapperDetailedNoArgs(cart, database, "", buf, FALSE, FALSE, FALSE, FALSE);
hPrintf("<div style='max-width:1080px;'>");
hPrintf("<form action='%s' name='%s' id='%s' method='get'>\n\n", hgTracksName(),TRACK_SEARCH_FORM,TRACK_SEARCH_FORM);
cartSaveSession(cart); // Creates hidden var of hgsid to avoid bad voodoo
safef(buf, sizeof(buf), "%lu", clock1());
cgiMakeHiddenVar("hgt_", buf); // timestamps page to avoid browser cache
hPrintf("<input type='hidden' name='db' value='%s'>\n", database);
hPrintf("<input type='hidden' name='%s' id='currentTab' value='%s'>\n", TRACK_SEARCH_CURRENT_TAB, currentTab);
hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_DEL_ROW);
hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_ADD_ROW);
hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_PAGER);
hPrintf("<div id='tabs' style='display:none; %s'>\n"
"<ul>\n"
"<li><a href='#simpleTab'><B style='font-size:.9em;font-family: arial, Geneva, Helvetica, san-serif;'>Search</B></a></li>\n"
"<li><a href='#advancedTab'><B style='font-size:.9em;font-family: arial, Geneva, Helvetica, san-serif;'>Advanced</B></a></li>\n"
"</ul>\n"
"<div id='simpleTab' style='max-width:inherit;'>\n",cgiBrowser()==btIE?"width:1060px;":"max-width:inherit;");
hPrintf("<table style='width:100%%; font-size:.9em;'><tr><td colspan='2'>");
hPrintf("<input type='text' name='%s' id='simpleSearch' class='submitOnEnter' value='%s' style='max-width:1000px; width:100%%;' onkeyup='findTracksSearchButtonsEnable(true);'>\n",
TRACK_SEARCH_SIMPLE,descSearch == NULL ? "" : descSearch);
if (simpleSearch && descSearch)
searchTermsExist = TRUE;
hPrintf("</td></tr><td style='max-height:4px;'></td></tr></table>");
//hPrintf("</td></tr></table>");
hPrintf("<input type='submit' name='%s' id='searchSubmit' value='search' style='font-size:.8em;'>\n", TRACK_SEARCH);
hPrintf("<input type='button' name='clear' value='clear' class='clear' style='font-size:.8em;' onclick='findTracksClear();'>\n");
hPrintf("<input type='submit' name='submit' value='cancel' class='cancel' style='font-size:.8em;'>\n");
hPrintf("</div>\n");
// Advanced tab
hPrintf("<div id='advancedTab' style='width:inherit;'>\n"
"<table cellSpacing=0 style='width:inherit; font-size:.9em;'>\n");
cols = 8;
// Track Name contains
hPrintf("<tr><td colspan=3></td>");
hPrintf("<td nowrap><b style='max-width:100px;'>Track Name:</b></td>");
hPrintf("<td align='right'>contains</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
hPrintf("<input type='text' name='%s' id='nameSearch' class='submitOnEnter' value='%s' onkeyup='findTracksSearchButtonsEnable(true);' style='min-width:326px; font-size:.9em;'>",
TRACK_SEARCH_ON_NAME, nameSearch == NULL ? "" : nameSearch);
hPrintf("</td></tr>\n");
// Description contains
hPrintf("<tr><td colspan=2></td><td align='right'>and </td>");
hPrintf("<td><b style='max-width:100px;'>Description:</b></td>");
hPrintf("<td align='right'>contains</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
hPrintf("<input type='text' name='%s' id='descSearch' value='%s' class='submitOnEnter' onkeyup='findTracksSearchButtonsEnable(true);' style='max-width:536px; width:536px; font-size:.9em;'>",
TRACK_SEARCH_ON_DESCR, descSearch == NULL ? "" : descSearch);
hPrintf("</td></tr>\n");
if (!simpleSearch && descSearch)
searchTermsExist = TRUE;
hPrintf("<tr><td colspan=2></td><td align='right'>and </td>\n");
hPrintf("<td><b style='max-width:100px;'>Group:</b></td>");
hPrintf("<td align='right'>is</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
cgiMakeDropListFull(TRACK_SEARCH_ON_GROUP, labels, groups, numGroups, groupSearch, "class='groupSearch' style='min-width:40%; font-size:.9em;'");
hPrintf("</td></tr>\n");
if (!simpleSearch && groupSearch)
searchTermsExist = TRUE;
#ifdef TRACK_SEARCH_ON_TYPE
// Track Type is (drop down)
hPrintf("<tr><td colspan=2></td><td align='right'>and </td>\n");
hPrintf("<td nowrap><b style='max-width:100px;'>Data Format:</b></td>");
hPrintf("<td align='right'>is</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
char **formatTypes = NULL;
char **formatLabels = NULL;
int formatCount = getFormatTypes(&formatLabels, &formatTypes);
cgiMakeDropListFull(TRACK_SEARCH_ON_TYPE, formatLabels, formatTypes, formatCount, typeSearch, "class='typeSearch' style='min-width:40%; font-size:.9em;'");
hPrintf("</td></tr>\n");
if (!simpleSearch && typeSearch)
searchTermsExist = TRUE;
#endif///def TRACK_SEARCH_ON_TYPE
// Metadata selects require careful accounting
if(metaDbExists)
numMetadataSelects = printMdbSelects(conn, cart, simpleSearch, &mdbVar, &mdbVal, &numMetadataNonEmpty, cols);
else
numMetadataSelects = 0;
hPrintf("</table>\n");
hPrintf("<input type='submit' name='%s' id='searchSubmit' value='search' style='font-size:.8em;'>\n", TRACK_SEARCH);
hPrintf("<input type='button' name='clear' value='clear' class='clear' style='font-size:.8em;' onclick='findTracksClear();'>\n");
hPrintf("<input type='submit' name='submit' value='cancel' class='cancel' style='font-size:.8em;'>\n");
//hPrintf("<a target='_blank' href='../goldenPath/help/trackSearch.html'>help</a>\n");
hPrintf("</div>\n</div>\n");
hPrintf("</form>\n");
hPrintf("</div>"); // Restricts to max-width:1000px;
if(descSearch != NULL && !strlen(descSearch))
descSearch = NULL;
if(groupSearch != NULL && sameString(groupSearch, ANYLABEL))
groupSearch = NULL;
if(typeSearch != NULL && sameString(typeSearch, ANYLABEL))
typeSearch = NULL;
if(!isEmpty(descSearch))
{
char *tmp = cloneString(descSearch);
char *val = nextWord(&tmp);
struct slName *el, *descList = NULL;
int i;
while (val != NULL)
{
slNameAddTail(&descList, val);
descWordCount++;
val = nextWord(&tmp);
}
descWords = needMem(sizeof(char *) * descWordCount);
for(i = 0, el = descList; el != NULL; i++, el = el->next)
descWords[i] = strLower(el->name);
}
if (doSearch && simpleSearch && descWordCount <= 0)
doSearch = FALSE;
if(doSearch)
{
// Now search
struct slRef *tracks = NULL;
if(simpleSearch)
tracks = simpleSearchForTracksstruct(trix,descWords,descWordCount);
else
tracks = advancedSearchForTracks(conn,groupList,descWords,descWordCount,nameSearch,typeSearch,descSearch,groupSearch,numMetadataNonEmpty,numMetadataSelects,mdbVar,mdbVal);
// Sort and Print results
enum sortBy sortBy = cartUsualInt(cart,TRACK_SEARCH_SORT,sbRelevance);
tracksFound = slCount(tracks);
if(tracksFound > 1)
findTracksSort(&tracks,simpleSearch,sortBy);
displayFoundTracks(cart,tracks,tracksFound,sortBy);
}
hFreeConn(&conn);
webNewSection("About Track Search");
if(metaDbExists)
hPrintf("<p>Search for terms in track names, descriptions, groups, and ENCODE "
"metadata. If multiple terms are entered, only tracks with all terms "
"will be part of the results.");
else
hPrintf("<p>Search for terms in track descriptions, groups, and names. "
"If multiple terms are entered, only tracks with all terms "
"will be part of the results.");
hPrintf("<BR><a target='_blank' href='../goldenPath/help/trackSearch.html'>more help</a></p>\n");
webEndSectionTables();
}
static void displayFoundTracks(struct cart *cart, struct slRef *tracks, int tracksFound,enum sortBy sortBy)
// Routine for displaying found tracks
{
hPrintf("<div id='found' style='display:none;'>\n"); // This div allows the clear button to empty it
if(tracksFound < 1)
{
hPrintf("<p>No tracks found</p>\n");
}
else
{
struct hash *tdbHash = makeTrackHash(database, chromName);
hPrintf("<form action='%s' name='%s' id='%s' method='post'>\n\n", hgTracksName(),SEARCH_RESULTS_FORM,SEARCH_RESULTS_FORM);
cartSaveSession(cart); // Creates hidden var of hgsid to avoid bad voodoo
int startFrom = 0;
hPrintf("<table id='foundTracks'>\n");
// Opening view in browser button and foundTracks count
#define ENOUGH_FOUND_TRACKS 10
if(tracksFound >= ENOUGH_FOUND_TRACKS)
{
hPrintf("<tr><td nowrap colspan=3>\n");
hPrintf("<INPUT TYPE=SUBMIT NAME='submit' VALUE='return to browser' class='viewBtn' style='font-size:.8em;'>");
hPrintf(" <FONT class='selCbCount'></font>\n");
startFrom = cartUsualInt(cart,TRACK_SEARCH_PAGER,0);
if (startFrom > 0 && startFrom < tracksFound)
{
int countUp = 0;
for(countUp=0; countUp < startFrom;countUp++)
{
if (slPopHead(&tracks) == NULL) // memory waste
break;
}
}
hPrintf("</td><td align='right' valign='bottom'>\n");
findTracksPageLinks(tracksFound,startFrom);
hPrintf("</td></tr>\n");
}
// Begin foundTracks table
//hPrintf("<table id='foundTracks'><tr><td colspan='2'>\n");
hPrintf("<tr><td colspan='2'>\n");
hPrintf("</td><td align='right'>\n");
#define PM_BUTTON "<IMG height=18 width=18 onclick=\"return findTracksCheckAllWithWait(%s);\" id='btn_%s' src='../images/%s' title='%s all found tracks'>"
hPrintf("</td></tr><tr bgcolor='#%s'><td>",HG_COL_HEADER);
hPrintf(PM_BUTTON,"true", "plus_all", "add_sm.gif", "Select");
hPrintf(PM_BUTTON,"false","minus_all","remove_sm.gif","Unselect");
hPrintf("</td><td><b>Visibility</b></td><td colspan=2> <b>Track Name</b>\n");
// Sort options?
if(tracksFound >= ENOUGH_FOUND_TRACKS)
{
hPrintf("<span style='float:right;'>Sort:");
cgiMakeOnClickRadioButton(TRACK_SEARCH_SORT, "0", (sortBy == sbRelevance),"onchange=\"findTracksSortNow(this);\"");
hPrintf("by Relevance");
cgiMakeOnClickRadioButton(TRACK_SEARCH_SORT, "1", (sortBy == sbAbc), "onchange=\"findTracksSortNow(this);\"");
hPrintf("Alphabetically");
cgiMakeOnClickRadioButton(TRACK_SEARCH_SORT, "2",(sortBy == sbHierarchy), "onchange=\"findTracksSortNow(this);\"");
hPrintf("by Hierarchy </span>\n");
}
hPrintf("</td></tr>\n");
// Set up json for js functionality
struct dyString *jsonTdbVars = NULL;
int trackCount=0;
boolean containerTrackCount = 0;
struct slRef *ptr;
while((ptr = slPopHead(&tracks)))
{
if(++trackCount > MAX_FOUND_TRACKS)
break;
struct track *track = (struct track *) ptr->val;
jsonTdbSettingsBuild(&jsonTdbVars, track, FALSE); // FALSE: No configuration from track search
if (tdbIsFolder(track->tdb)) // supertrack
hPrintf("<tr bgcolor='%s' valign='top' class='found'>\n","#EED5B7");//"#DEB887");//"#E6B426");//#FCECC0//COLOR_LTGREY);//COLOR_LTGREEN);//COLOR_TRACKLIST_LEVEL1);
else if (tdbIsContainer(track->tdb))
hPrintf("<tr bgcolor='%s' valign='top' class='found'>\n",COLOR_TRACKLIST_LEVEL3);
else
hPrintf("<tr bgcolor='%s' valign='top' class='found'>\n",COLOR_TRACKLIST_LEVEL2);
hPrintf("<td align='center'>\n");
// Determine visibility and checked state
track->visibility = tdbVisLimitedByAncestors(cart, track->tdb, TRUE, TRUE);
boolean checked = ( track->visibility != tvHide );
if(tdbIsContainerChild(track->tdb))
{
checked = fourStateVisible(subtrackFourStateChecked(track->tdb,cart)); // Don't need all 4 states here. Visible=checked&&enabled
checked = (checked && ( track->visibility != tvHide )); // Checked is only if subtrack level vis is also set!
}
// Setup the check box
#define CB_HIDDEN_VAR "<INPUT TYPE=HIDDEN disabled=true NAME='%s_sel' VALUE='%s'>"
if (tdbIsContainerChild(track->tdb) || tdbIsFolderContent(track->tdb)) // subtracks and folder children get "_sel" var. ("_sel" var is temporary on folder children)
hPrintf(CB_HIDDEN_VAR,track->track,checked?"1":CART_VAR_EMPTY);
#define CB_SEEN "<INPUT TYPE=CHECKBOX id='%s_sel_id' VALUE='on' class='selCb' onclick='findTracksClickedOne(this,true);'%s>"
hPrintf(CB_SEEN,track->track,(checked?" CHECKED":""));
hPrintf("</td><td>\n");
// Setup the visibility drop down
#define VIS_HIDDEN_VAR "<INPUT TYPE=HIDDEN disabled=true NAME='%s' VALUE='%s'>"
hPrintf(VIS_HIDDEN_VAR,track->track,CART_VAR_EMPTY); // All tracks get vis hidden var
char extra[512];
if (tdbIsFolder(track->tdb))
{
safef(extra,sizeof(extra),"id='%s_id' onchange='findTracksChangeVis(this)'",track->track);
hideShowDropDownWithClassAndExtra(track->track, (track->visibility != tvHide), "normalText visDD",extra);
}
else
{
safef(extra,sizeof(extra),"id='%s_id' onchange='findTracksChangeVis(this)'",track->track);
hTvDropDownClassWithJavascript(NULL, track->visibility,track->canPack,"normalText seenVis",extra);
}
// If this is a container track, allow configuring...
if (tdbIsContainer(track->tdb) || tdbIsFolder(track->tdb))
{
containerTrackCount++;
hPrintf(" <a href='hgTrackUi?db=%s&g=%s&%s=Search' title='Configure this container track...'><IMG SRC='../images/folderWrench.png'></a> ",database,track->track,TRACK_SEARCH);
}
hPrintf("</td>\n");
// shortLabel has description popup and longLabel has "..." metadata
hPrintf("<td><a target='_top' onclick=\"hgTrackUiPopUp('%s',true); return false;\" href='%s' title='Display track details'>%s</a></td>\n", track->track, trackUrl(track->track, NULL), track->shortLabel);
hPrintf("<td>%s", track->longLabel);
compositeMetadataToggle(database, track->tdb, "...", TRUE, FALSE, tdbHash);
hPrintf("</td></tr>\n");
}
//hPrintf("</table>\n");
// Closing view in browser button and foundTracks count
hPrintf("<tr><td nowrap colspan=3>");
hPrintf("<INPUT TYPE=SUBMIT NAME='submit' VALUE='Return to Browser' class='viewBtn' style='font-size:.8em;'>");
hPrintf(" <FONT class='selCbCount'></font>");
if(tracksFound >= ENOUGH_FOUND_TRACKS)
{
hPrintf("</td><td align='right' valign='top'>\n");
findTracksPageLinks(tracksFound,startFrom);
hPrintf("</td></tr>\n");
}
hPrintf("</table>\n");
if(containerTrackCount > 0)
hPrintf("<BR><IMG SRC='../images/folderWrench.png'> Tracks so marked are containers which group related data tracks. Containers may need additional configuration (by clicking on the <IMG SRC='../images/folderWrench.png'> icon) before they can be viewed in the browser.<BR>\n");
//hPrintf("* Tracks so marked are containers which group related data tracks. These may not be visible unless further configuration is done. Click on the * to configure these.<BR><BR>\n");
hPrintf("\n</form>\n");
// be done with json
hWrites(jsonTdbSettingsUse(&jsonTdbVars));
}
#ifdef OMIT
if(!doSearch)
{
hPrintf("<p><b>Recently Done</b><ul>\n"
"<li>Can now page through found tracks 100 at a time.</li>"
"<li>Added <IMG SRC='../images/folderWrench.png'> icon for contqainers with a configuration link. Is this okay?</li>"
"<li>SuperTracks can now be found.</li>"
"<li>Configuration of superTrack children's vis should result in proper superTrack reshaping. (This is really an hgTrackUi feature.)</li>"
"<li>Added sort toggle: Relevance, Alphabetically or by Hierarchy.</li>"
"<li>Composite/view visibilites in hgTrackUi get reshaped to reflect found/selected subtracks. (In demo1: only default state composites; demo2: all composites.)</li>"
"<li>Non-data 'container' tracks (composites and supertracks) have '*' to mark them, and can be configured before displaying. Better suggestions?</li>"
"</ul></p>"
"<p><b>Suggested improvments:</b><ul>\n"
"<li>The metadata values will not be white-listed, but it would be nice to have more descriptive text for them. A short label added to cv.ra?</li>"
"<li>Look and feel of found track list (here) and composite subtrack list (hgTrackUi) should converge. Jim suggests look and feel of hgTracks 'Configure Tracks...' list instead.</li>"
"<li>Drop-down list of terms (cells, antibodies, etc.) should be multi-select with checkBoxes as seen in filterComposites. Perhaps saved for v2.0.</li>"
"</ul></p>\n");
}
#endif///def OMIT
hPrintf("</div>"); // This div allows the clear button to empty it
}