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);
}
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 stopUpload(struct sqlConnection *conn)
/* Try and stop current upload. */
{
char *url = trimSpaces(cgiString("url"));
cgiMakeHiddenVar("url", url);
struct edwSubmit *sub = edwMostRecentSubmission(conn, url);
if (sub == NULL)
{
/* Submission hasn't happened yet - remove it from job queue. */
unsigned edwSubmitJobId = 0;
int posInQueue = edwSubmitPositionInQueue(conn, url, &edwSubmitJobId);
if (posInQueue >= 0)
{
char query[256];
sqlSafef(query, sizeof(query), "delete from edwSubmitJob where id=%u", edwSubmitJobId);
sqlUpdate(conn, query);
printf("Removed submission from %s from job queue\n", url);
}
}
else
{
char query[256];
sqlSafef(query, sizeof(query),
"update edwSubmit set errorMessage='Stopped by user.' where id=%u", sub->id);
sqlUpdate(conn, query);
}
monitorSubmission(conn);
}
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 printGreatSubmitButtons()
/* print submit button to create data and then send query results to GREAT. */
{
cartSetString(cart, hgtaCompressType, textOutCompressNone);
cartSetString(cart, hgtaOutFileName, "");
cgiMakeHiddenVar(hgtaCompressType, textOutCompressNone);
cgiMakeHiddenVar(hgtaOutFileName, "");
cgiMakeHiddenVar(hgtaDoGreatOutput, "on");
cgiMakeHiddenVar(hgtaPrintCustomTrackHeaders, "on");
cgiMakeButton(hgtaDoGreatQuery, "Send query to GREAT");
hPrintf("</FORM>\n");
hPrintf(" ");
/* new form as action is different */
hPrintf("<FORM ACTION=\"%s\" METHOD=GET>\n", cgiScriptName());
cgiMakeButton(hgtaDoMainPage, "Cancel");
hPrintf("</FORM>\n");
}
/* This is very similar to doForm except it's for Zoo species */
void doFormZoo(struct cart *lCart)
/** Print out the form for users */
{
char **genomeList = NULL;
int genomeCount = 0;
char *dbChoice = NULL;
int i = 0;
cart = lCart;
cartWebStart(cart, databases, "Converting Coordinates Between Species");
puts(
"<p>This page attempts to convert coordinates from one Zoo species' CFTR region\n"
"to another. The mechanism for doing this is to use the blastz alignments which have been\n"
"done between each Zoo species and use this to convert coordinates. In general these should\n"
"be reasonable conversions however the user is advised to not take the conversions as absolute \n"
"standards. Furthermore a given region from a given species is not necessarily alignable to any\n"
"region in a different species.\n"
);
/* Get all Zoo species since we are using blastz static alignments */
getIndexedGenomeDescriptionsZoo(&genomeList, &genomeCount,FALSE);
/* choose whether to use the db supplied by cgi or our default */
if(origDb != NULL && strstr(origDb, "zoo") == NULL)
errAbort("Sorry, this mode of the program only works between zoo species.");
dbChoice = chooseDb(origDb, genomeList[0]);
printf("<form action=\"../cgi-bin/hgCoordConv\" method=get>\n");
printf("<br><br>\n");
printf("<table><tr>\n");
printf("<b><td><table><tr><td>Original Species: </b>\n");
cgiMakeDropList("origGenome", genomeList, genomeCount, dbChoice);
printf("</td></tr></table></td>\n");
printf(" <b><td><table><tr><td>Original Position: </b>\n");
/* if someone has passed in a position fill it in for them */
if(position == NULL)
cgiMakeTextVar("position",defaultPos, 30);
else
cgiMakeTextVar("position",position, 30);
printf("</td></tr></table></td>\n");
printf("<b><td><table><tr><td>New Species: </b>\n");
freez(&genomeList);
genomeCount =0;
getIndexedGenomeDescriptionsZoo(&genomeList, &genomeCount, FALSE);
cgiMakeDropList("newGenome", genomeList, genomeCount, genomeList[genomeCount -1]);
printf("</td></tr></table></td></tr>\n");
printf("<tr><td colspan=6 align=right><br>\n");
cgiMakeButton("Submit","submit");
printf("</center></td></tr></table>\n");
cgiMakeHiddenVar("calledSelf", "on");
printf("</form>\n");
cartWebEnd();
}
void doForm(struct cart *lCart)
/** Print out the form for users */
{
char **genomeList = NULL;
int genomeCount = 0;
char *dbChoice = NULL;
int i = 0;
cart = lCart;
cartWebStart(cart, databases, "Converting Coordinates Between Drafts");
puts(
"<p>This page attempts to convert coordinates from one draft of the human genome\n"
"to another. The mechanism for doing this is to cut out and align pieces from the\n"
"old draft and align them to the new draft making sure that\n"
"they are in the same order and orientation. In general the smaller the sequence the better\n"
"the chances of successful conversion.\n"
);
getIndexedGenomeDescriptions(&genomeList, &genomeCount, TRUE);
/* choose whether to use the db supplied by cgi or our default */
if(origDb != NULL && strstr(origDb, "hg") == NULL)
errAbort("Sorry, currently the conversion program only works with human genomes.");
dbChoice = chooseDb(origDb, genomeList[0]);
printf("<form action=\"../cgi-bin/hgCoordConv\" method=get>\n");
printf("<br><br>\n");
printf("<table><tr>\n");
printf("<b><td><table><tr><td>Original Draft: </b>\n");
cgiMakeDropList("origGenome", genomeList, genomeCount, dbChoice);
printf("</td></tr></table></td>\n");
printf(" <b><td><table><tr><td>Original Position: </b>\n");
/* if someone has passed in a position fill it in for them */
if(position == NULL)
cgiMakeTextVar("position",defaultPos, 30);
else
cgiMakeTextVar("position",position, 30);
printf("</td></tr></table></td>\n");
printf("<b><td><table><tr><td>New Draft: </b>\n");
freez(&genomeList);
genomeCount =0;
getIndexedGenomeDescriptions(&genomeList, &genomeCount, TRUE);
cgiMakeDropList("newGenome", genomeList, genomeCount, genomeList[genomeCount -1]);
printf("</td></tr></table></td></tr>\n");
printf("<tr><td colspan=6 align=right><br>\n");
cgiMakeButton("Submit","submit");
printf("</center></td></tr></table>\n");
cgiMakeHiddenVar("calledSelf", "on");
printf("</form>\n");
cartWebEnd();
}
void relativeScroll(double amount)
/* Scroll percentage of visible window. */
{
trackOrigOffset = trackOrigOffset + (int)(amount*MAX_PB_PIXWIDTH);
/* Make sure don't scroll of ends. */
if (trackOrigOffset > ((pbScale* protSeqLen) - 600))
trackOrigOffset = pbScale*protSeqLen - 700;
if (trackOrigOffset < 0) trackOrigOffset = 0;
safef(pbScaleStr, sizeof(pbScaleStr), "%d", pbScale);
cgiMakeHiddenVar("pbScaleStr", pbScaleStr);
}
void doGreatTopLevel()
/* intermediate page for formats printed directly from top form */
{
struct dyString *name = getRequestName();
htmlOpen("Send BED data to GREAT as %s", dyStringContents(name));
freeDyString(&name);
verifyGreatAssemblies();
startGreatForm();
cgiMakeHiddenVar(hgtaDoTopSubmit, "get output");
printGreatSubmitButtons();
hPrintf("<div style='height:.9em;'></div>\n");
htmlClose();
}
void jsMakeTrackingCheckBox(struct cart *cart,
char *cgiVar, char *jsVar, boolean usualVal)
/* Make a check box filling in with existing value and
* putting a javascript tracking variable on it. */
{
char buf[256];
boolean oldVal = cartUsualBoolean(cart, cgiVar, usualVal);
jsInlineF("var %s=%d;\n", jsVar, oldVal);
hPrintf("<INPUT TYPE=CHECKBOX NAME='%s' ID='%s' VALUE=1", cgiVar, cgiVar);
if (oldVal)
hPrintf(" CHECKED");
hPrintf(">");
jsOnEventByIdF("click", cgiVar, "%s=(%s+1)%%2;", jsVar, jsVar);
safef(buf, sizeof(buf), "%s%s", cgiBooleanShadowPrefix(), cgiVar);
cgiMakeHiddenVar(buf, "0");
}
void jsMakeSetClearButton(struct cart *cart,
char *form, char *buttonVar, char *buttonLabel,
char *cartVarPrefix, struct slName *cartVarSuffixList,
char *anchor, boolean currentPos, boolean isSet)
/* Make a button for setting or clearing all of a list of boolean
* cart variables (i.e. checkboxes). If this button was just pressed,
* set or clear those cart variables.
* Optional html anchor is appended to the form's action if given.
* If currentPos, anchor is ignored and jsSetVerticalPosition is used so
* that the new page gets the same vertical offset as the current page. */
{
struct slName *suffix;
char javascript[2048];
char *vertPosJs = "";
if (currentPos)
{
anchor = NULL;
jsInit();
vertPosJs = jsSetVerticalPosition(form);
}
cgiMakeHiddenVar(buttonVar, "");
safef(javascript, sizeof javascript,
"document.%s.action = '%s%s%s'; document.%s.%s.value='%s'; %s"
"document.%s.submit();",
form, cgiScriptName(),
(isNotEmpty(anchor) ? "#" : ""), (isNotEmpty(anchor) ? anchor : ""),
form, buttonVar, buttonLabel, vertPosJs, form);
cgiMakeOnClickButton(javascript, buttonLabel);
if (isNotEmpty(cgiOptionalString(buttonVar)))
{
char option[1024];
if (cartVarPrefix == NULL)
cartVarPrefix = "";
for (suffix = cartVarSuffixList; suffix != NULL; suffix = suffix->next)
{
safef(option, sizeof(option), "%s%s", cartVarPrefix, suffix->name);
cartSetBoolean(cart, option, isSet);
}
}
}
void eqFilterOption(char *db, char *table, char *field,
char *fieldLabel1, char *fieldLabel2, char *logOp)
/* Print out a table row with filter constraint options for an equality
* comparison. */
{
char *name;
hPrintf("<TR VALIGN=BOTTOM><TD> %s </TD><TD>\n", fieldLabel1);
puts(" is ");
name = filterFieldVarName(db, table, field, filterCmpVar);
cgiMakeDropList(name, eqOpMenu, eqOpMenuSize,
cartUsualString(cart, name, eqOpMenu[0]));
/* make a dummy pat_ CGI var for consistency with other filter options */
name = filterPatternVarName(db, table, field);
cgiMakeHiddenVar(name, "0");
hPrintf("</TD><TD>\n");
hPrintf("%s\n", fieldLabel2);
if (logOp == NULL)
logOp = "";
hPrintf("<TD>%s</TD></TR>\n", logOp);
}
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 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 doGetPrimers(char *db, char *organism, struct pcrServer *serverList,
char *fPrimer, char *rPrimer, int maxSize, int minPerfect, int minGood,
boolean flipReverse)
/* Put up form to get primers. */
{
redoDbAndOrgIfNoServer(serverList, &db, &organism);
struct sqlConnection *conn = hConnectCentral();
boolean gotTargetDb = sqlTableExists(conn, "targetDb");
hDisconnectCentral(&conn);
printf("<FORM ACTION=\"../cgi-bin/hgPcr\" METHOD=\"GET\" NAME=\"mainForm\">\n");
cartSaveSession(cart);
printf("<TABLE BORDER=0 WIDTH=\"96%%\" COLS=7><TR>\n");
printf("%s", "<TD><CENTER>\n");
printf("Genome:<BR>");
showGenomes(organism, serverList);
printf("%s", "</TD>\n");
printf("%s", "<TD><CENTER>\n");
printf("Assembly:<BR>");
showAssemblies(organism, db, serverList, gotTargetDb);
printf("%s", "</TD>\n");
if (gotTargetDb)
{
struct targetPcrServer *targetServerList = getTargetServerList(db, NULL);
if (targetServerList != NULL)
{
char *target = cartUsualString(cart, "wp_target", "genome");
printf("%s", "<TD><CENTER>\n");
printf("Target:<BR>");
showTargets(target, targetServerList);
printf("%s", "</TD>\n");
}
else
cgiMakeHiddenVar("wp_target", "genome");
}
else
cgiMakeHiddenVar("wp_target", "genome");
printf("%s", "<TD COLWIDTH=2><CENTER>\n");
printf("Forward Primer:<BR>");
cgiMakeTextVar("wp_f", fPrimer, 22);
printf("%s", "</TD>\n");
printf("%s", "<TD><CENTER COLWIDTH=2>\n");
printf(" Reverse Primer:<BR>");
cgiMakeTextVar("wp_r", rPrimer, 22);
printf("%s", "</TD>\n");
printf("%s", "<TD><CENTER>\n");
printf(" <BR>");
cgiMakeButton("Submit", "submit");
printf("%s", "</TD>\n");
printf("</TR></TABLE><BR>");
printf("<TABLE BORDER=0 WIDTH=\"96%%\" COLS=4><TR>\n");
printf("%s", "<TD><CENTER>\n");
printf("Max Product Size: ");
cgiMakeIntVar("wp_size", maxSize, 5);
printf("%s", "</TD>\n");
printf("%s", "<TD><CENTER>\n");
printf(" Min Perfect Match: ");
cgiMakeIntVar("wp_perfect", minPerfect, 2);
printf("%s", "</TD>\n");
printf("%s", "<TD><CENTER>\n");
printf(" Min Good Match: ");
cgiMakeIntVar("wp_good", minGood, 2);
printf("%s", "</TD>\n");
printf("%s", "<TD><CENTER>\n");
printf(" Flip Reverse Primer: ");
cgiMakeCheckBox("wp_flipReverse", flipReverse);
printf("%s", "</TD>\n");
printf("</TR></TABLE><BR>");
printf("</FORM>\n");
/* Put up a second form who's sole purpose is to preserve state
* when the user flips the genome button. */
printf("<FORM ACTION=\"../cgi-bin/hgPcr\" METHOD=\"GET\" NAME=\"orgForm\">"
"<input type=\"hidden\" name=\"wp_target\" value=\"\">\n"
"<input type=\"hidden\" name=\"db\" value=\"\">\n"
"<input type=\"hidden\" name=\"org\" value=\"\">\n"
"<input type=\"hidden\" name=\"wp_f\" value=\"\">\n"
"<input type=\"hidden\" name=\"wp_r\" value=\"\">\n"
"<input type=\"hidden\" name=\"wp_size\" value=\"\">\n"
"<input type=\"hidden\" name=\"wp_perfect\" value=\"\">\n"
"<input type=\"hidden\" name=\"wp_good\" value=\"\">\n"
"<input type=\"hidden\" name=\"wp_showPage\" value=\"true\">\n");
cartSaveSession(cart);
printf("</FORM>\n");
webNewSection("About In-Silico PCR");
doHelp();
printf("%s", "<P><H3>Author</H3>\n");
printf("%s", "<P>In-Silico PCR was written by "
"<A HREF=\"mailto:[email protected]\">Jim Kent</A>.\n"
"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. Contact Jim for details.</P>\n");
}
void doTracks(char *proteinID, char *mrnaID, char *aa, int *yOffp, char *psOutput)
/* draw various protein tracks */
{
int l;
char aaOrigOffsetStr[20];
int hasResFreq;
char uniProtDbName[50];
char *protDbDate;
char *chrom;
char strand;
char *kgId, *kgPep, *protPep;
char cond_str[255];
char *answer;
//int i, ll;
//char *chp1, *chp2;
g_font = mgSmallFont();
safef(pbScaleStr, sizeof(pbScaleStr), "%d", pbScale);
if (psOutput != NULL)
{
pbScale = atoi(cartOptionalString(cart, "pbt.pbScaleStr"));
}
if (cgiOptionalString("trackOffset") != NULL)
{
trackOrigOffset = atoi(cgiOptionalString("trackOffset"));
}
if (cgiOptionalString("pbScaleStr") != NULL)
{
pbScale = atoi(cgiOptionalString("pbScaleStr"));
}
if (cgiOptionalString("pbScale") != NULL)
{
scaleButtonPushed = TRUE;
if (strcmp(cgiOptionalString("pbScale"), "1/6") == 0) pbScale = 1;
if (strcmp(cgiOptionalString("pbScale"), "1/2") == 0) pbScale = 3;
if (strcmp(cgiOptionalString("pbScale"), "FULL") == 0) pbScale = 6;
if (strcmp(cgiOptionalString("pbScale"), "DNA") == 0) pbScale =22;
safef(pbScaleStr, sizeof(pbScaleStr), "%d", pbScale);
cgiMakeHiddenVar("pbScaleStr", pbScaleStr);
}
else
{
scaleButtonPushed = FALSE;
}
if (psOutput == NULL)
{
if (cgiVarExists("pbt.left3"))
{
relativeScroll(-0.95);
initialWindow = FALSE;
}
else if (cgiVarExists("pbt.left2"))
{
relativeScroll(-0.475);
initialWindow = FALSE;
}
else if (cgiVarExists("pbt.left1"))
{
relativeScroll(-0.02);
initialWindow = FALSE;
}
else if (cgiVarExists("pbt.right1"))
{
relativeScroll(0.02);
initialWindow = FALSE;
}
else if (cgiVarExists("pbt.right2"))
{
relativeScroll(0.475);
initialWindow = FALSE;
}
else if (cgiVarExists("pbt.right3"))
{
relativeScroll(0.95);
initialWindow = FALSE;
}
}
dnaUtilOpen();
l=strlen(aa);
/* initialize AA properties */
aaPropertyInit(&hasResFreq);
sfCount = getSuperfamilies2(proteinID);
if (sfCount == 0)
{
sfCount = getSuperfamilies(proteinID);
}
if (mrnaID != NULL)
{
if (kgVersion == KG_III)
{
doExonTrack = FALSE;
sqlSafefFrag(cond_str, sizeof(cond_str), "spId='%s'", proteinID);
kgId = sqlGetField(database, "kgXref", "kgId", cond_str);
if (kgId != NULL)
{
sqlSafefFrag(cond_str, sizeof(cond_str), "name='%s'", kgId);
kgPep = sqlGetField(database, "knownGenePep", "seq", cond_str);
//printf("<pre><br>%s", kgPep);fflush(stdout);
if (kgPep != NULL)
{
if (strstr(protDbName, "proteins") != NULL)
{
protDbDate = strstr(protDbName, "proteins") + strlen("proteins");
safef(uniProtDbName, sizeof(uniProtDbName),"sp%s", protDbDate);
sqlSafefFrag(cond_str, sizeof(cond_str), "acc='%s'", proteinID);
protPep = sqlGetField(uniProtDbName, "protein", "val", cond_str);
//printf("<br>%s\n", protPep);fflush(stdout);
if (protPep != NULL)
{
if (sameWord(kgPep, protPep))
{
//printf("<br>MATCH!\n");fflush(stdout);
sqlSafefFrag(cond_str, sizeof(cond_str), "qName='%s'", kgId);
answer = sqlGetField(database, kgProtMapTableName,
"qName", cond_str);
if (answer != NULL)
{
/* NOTE: passing in kgId instead of proteinID because
kgProtMap2's qName uses kgId instead of
protein display ID */
getExonInfo(kgId, &exCount, &chrom, &strand);
assert(exCount > 0);
doExonTrack = TRUE;
}
}
/*
else
{
chp1 = kgPep;
printf("<br>");
chp2 = protPep;
ll = strlen(kgPep);
if (strlen(protPep) < ll) ll= strlen(protPep);
for (i=0; i<ll; i++)
{
if (*chp1 != *chp2)
{
printf("%c", *chp1);
}
else
{
printf(".");
}
chp1++; chp2++;
}
}
//printf("</pre>");fflush(stdout);
*/
}
}
}
}
}
else
{
doExonTrack = TRUE;
getExonInfo(proteinID, &exCount, &chrom, &strand);
assert(exCount > 0);
}
/* do the following only if pbTracks called doTracks() */
if (initialWindow && IAmPbTracks)
{
prevGBOffsetSav = calPrevGB(exCount, chrom, strand, l, yOffp, proteinID, mrnaID);
trackOrigOffset = prevGBOffsetSav;
if (trackOrigOffset > (protSeqLen*pbScale - 600))
trackOrigOffset = protSeqLen*pbScale - 600;
/* prevent negative value */
if (trackOrigOffset < 0) trackOrigOffset = 0;
}
/* if this if for PDF/Postscript, the trackOrigOffset is already calculated previously,
use the saved value */
if (psOutput != NULL)
{
trackOrigOffset = atoi(cartOptionalString(cart, "pbt.trackOffset"));
}
}
/*printf("<br>%d %d<br>%d %d\n", prevGBStartPos, prevGBEndPos,
blockGenomeStartPositive[exCount-1], blockGenomeStartPositive[0]); fflush(stdout);
*/
if (strand == '-')
{
if ((prevGBStartPos <= blockGenomeStartPositive[exCount-1]) && (prevGBEndPos >= blockGenomeStartPositive[0]))
{
showPrevGBPos = FALSE;
}
}
else
{
if ((prevGBStartPos <= blockGenomeStartPositive[0]) && (prevGBEndPos >= blockGenomeStartPositive[exCount-1]))
{
showPrevGBPos = FALSE;
}
}
if ((cgiOptionalString("aaOrigOffset") != NULL) && scaleButtonPushed)
{
trackOrigOffset = atoi(cgiOptionalString("aaOrigOffset"))*pbScale;
}
pixWidth = 160+ protSeqLen*pbScale;
if (pixWidth > MAX_PB_PIXWIDTH)
{
pixWidth = MAX_PB_PIXWIDTH;
}
if ((protSeqLen*pbScale - trackOrigOffset) < MAX_PB_PIXWIDTH)
{
pixWidth = protSeqLen*pbScale - trackOrigOffset + 160;
}
if (pixWidth < 550) pixWidth = 550;
insideWidth = pixWidth-gfxBorder;
if (proteinInSupportedGenome)
{
pixHeight = 250;
}
else
{
pixHeight = 215;
}
if (sfCount > 0) pixHeight = pixHeight + 20;
/* make room for individual residues display */
if (pbScale >=6) pixHeight = pixHeight + 20;
if (pbScale >=18) pixHeight = pixHeight + 30;
if (psOutput)
{
vg = vgOpenPostScript(pixWidth, pixHeight, psOutput);
suppressHtml = TRUE;
hideControls = TRUE;
}
else
{
trashDirFile(&gifTn, "pbt", "pbt", ".png");
vg = vgOpenPng(pixWidth, pixHeight, gifTn.forCgi, FALSE);
}
/* Put up horizontal scroll controls. */
hWrites("Move ");
hButton("pbt.left3", "<<<");
hButton("pbt.left2", " <<");
hButton("pbt.left1", " < ");
hButton("pbt.right1", " > ");
hButton("pbt.right2", ">> ");
hButton("pbt.right3", ">>>");
hPrintf("     ");
/* Put up scaling controls. */
hPrintf("Current scale: ");
if (pbScale == 1) hPrintf("1/6 ");
if (pbScale == 3) hPrintf("1/2 ");
if (pbScale == 6) hPrintf("FULL ");
if (pbScale == 22) hPrintf("DNA ");
hPrintf("    Rescale to ");
hPrintf("<INPUT TYPE=SUBMIT NAME=\"pbScale\" VALUE=\"1/6\">\n");
hPrintf("<INPUT TYPE=SUBMIT NAME=\"pbScale\" VALUE=\"1/2\">\n");
hPrintf("<INPUT TYPE=SUBMIT NAME=\"pbScale\" VALUE=\"FULL\">\n");
if (kgVersion == KG_III)
{
/* for KG III, the protein has to exist in the kgProtMap2 table
(which will turn on doExonTrack flag)
to provide the genomic position data needed for DNA sequence display */
if ((proteinInSupportedGenome) && (doExonTrack))
hPrintf("<INPUT TYPE=SUBMIT NAME=\"pbScale\" VALUE=\"DNA\">\n");
}
else
{
if (proteinInSupportedGenome)
hPrintf("<INPUT TYPE=SUBMIT NAME=\"pbScale\" VALUE=\"DNA\">\n");
}
hPrintf("<FONT SIZE=1><BR><BR></FONT>\n");
g_vg = vg;
pbRed = vgFindColorIx(g_vg, 0xf9, 0x51, 0x59);
pbBlue = vgFindColorIx(g_vg, 0x00, 0x00, 0xd0);
bkgColor = vgFindColorIx(vg, 255, 254, 232);
vgBox(vg, 0, 0, insideWidth, pixHeight, bkgColor);
/* Start up client side map. */
hPrintf("<MAP Name=%s>\n", mapName);
vgSetClip(vg, 0, gfxBorder, insideWidth, pixHeight - 2*gfxBorder);
/* start drawing indivisual tracks */
doAAScale(l, yOffp, 1);
if (pbScale >= 6) doResidues(aa, l, yOffp);
if (pbScale >= 18) doDnaTrack(chrom, strand, exCount, l, yOffp);
if ((mrnaID != NULL) && showPrevGBPos)
{
doPrevGB(exCount, chrom, strand, l, yOffp, proteinID, mrnaID);
}
if (mrnaID != NULL)
{
if (doExonTrack) doExon(exCount, chrom, l, yOffp, proteinID, mrnaID);
}
doCharge(aa, l, yOffp);
doHydrophobicity(aa, l, yOffp);
doCysteines(aa, l, yOffp);
if (sfCount > 0) doSuperfamily(ensPepName, sfCount, yOffp);
if (hasResFreq) doAnomalies(aa, l, yOffp);
doAAScale(l, yOffp, -1);
vgClose(&vg);
/* Finish map and save out picture and tell html file about it. */
hPrintf("</MAP>\n");
/* put tracks image here */
hPrintf(
"\n<IMG SRC=\"%s\" BORDER=1 WIDTH=%d HEIGHT=%d USEMAP=#%s><BR>",
gifTn.forCgi, pixWidth, pixHeight, mapName);
if (proteinInSupportedGenome)
{
hPrintf("<A HREF=\"../goldenPath/help/pbTracksHelpFiles/pbTracksHelp.shtml#tracks\" TARGET=_blank>");
}
else
{
if (hIsGsidServer())
{
hPrintf("<A HREF=\"../goldenPath/help/pbTracksHelpFiles/pbGsid/pbTracksHelp.shtml#tracks\" TARGET=_blank>");
}
else
{
hPrintf("<A HREF=\"../goldenPath/help/pbTracksHelpFiles/pbTracksHelp.shtml#tracks\" TARGET=_blank>");
}
}
hPrintf("Explanation of Protein Tracks</A><br>");
safef(trackOffset, sizeof(trackOffset), "%d", trackOrigOffset);
cgiMakeHiddenVar("trackOffset", trackOffset);
/* remember where the AA base origin is so that it can be passed to next PB page */
aaOrigOffset = trackOrigOffset/pbScale;
safef(aaOrigOffsetStr, sizeof(aaOrigOffsetStr), "%d", aaOrigOffset);
cgiMakeHiddenVar("aaOrigOffset", aaOrigOffsetStr);
/* save the following state variables, to be used by PDF/Postcript processing */
cartSetString(cart,"pbt.pbScaleStr", pbScaleStr);
cartSetString(cart,"pbt.trackOffset", trackOffset);
cartSaveSession(cart);
fflush(stdout);
}
void doMiddle(struct cart *theCart)
/* Write header and body of html page. */
{
boolean gotDisconnect = FALSE;
cart = theCart;
if (cartVarExists(cart, hgHubDoClear))
{
doClearHub(cart);
cartWebEnd();
return;
}
if (cartVarExists(cart, hgHubDoDisconnect))
{
gotDisconnect = TRUE;
doDisconnectHub(cart);
// now rebuild the cart variable ("trackHubs") that has which lists which
// hubs are on.
hubConnectHubsInCart(cart);
}
if (cartVarExists(cart, hgHubDoReset))
{
doResetHub(cart);
}
cartWebStart(cart, NULL, "%s", pageTitle);
jsIncludeFile("jquery.js", NULL);
jsIncludeFile("utils.js", NULL);
jsIncludeFile("jquery-ui.js", NULL);
webIncludeResourceFile("jquery-ui.css");
jsIncludeFile("ajax.js", NULL);
jsIncludeFile("hgHubConnect.js", NULL);
jsIncludeFile("jquery.cookie.js", NULL);
printf("<div id=\"hgHubConnectUI\"> <div id=\"description\"> \n");
printf(
"<P>Track data hubs are collections of tracks from outside of UCSC that "
"can be imported into the Genome Browser. To import a public hub check "
"the box in the list below. "
"After import the hub will show up as a group of tracks with its own blue "
"bar and label underneath the main browser graphic, and in the "
"configure page. For more information, see the "
"<A HREF=\"../goldenPath/help/hgTrackHubHelp.html\" TARGET=_blank>"
"User's Guide</A>.</P>\n"
"<P><B>NOTE: Because Track Hubs are created and maintained by external sources,"
" UCSC is not responsible for their content.</B></P>"
);
printf("</div>\n");
getDbAndGenome(cart, &database, &organism, oldVars);
char *survey = cfgOptionEnv("HGDB_HUB_SURVEY", "hubSurvey");
char *surveyLabel = cfgOptionEnv("HGDB_HUB_SURVEY_LABEL", "hubSurveyLabel");
if (survey && differentWord(survey, "off"))
hPrintf("<span style='background-color:yellow;'><A HREF='%s' TARGET=_BLANK><EM><B>%s</EM></B></A></span>\n", survey, surveyLabel ? surveyLabel : "Take survey");
hPutc('\n');
// check to see if we have any new hubs
hubCheckForNew(cart);
// grab all the hubs that are listed in the cart
struct hubConnectStatus *hubList = hubConnectStatusListFromCartAll(cart);
checkTrackDbs(hubList);
// here's a little form for the add new hub button
printf("<FORM ACTION=\"%s\" NAME=\"addHubForm\">\n", "../cgi-bin/hgHubConnect");
cgiMakeHiddenVar("hubUrl", "");
cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on");
puts("</FORM>");
// this the form for the disconnect hub button
printf("<FORM ACTION=\"%s\" NAME=\"disconnectHubForm\">\n", "../cgi-bin/hgHubConnect");
cgiMakeHiddenVar("hubId", "");
cgiMakeHiddenVar(hgHubDoDisconnect, "on");
cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on");
puts("</FORM>");
// this the form for the reset hub button
printf("<FORM ACTION=\"%s\" NAME=\"resetHubForm\">\n", "../cgi-bin/hgHubConnect");
cgiMakeHiddenVar("hubUrl", "");
cgiMakeHiddenVar(hgHubDoReset, "on");
cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on");
puts("</FORM>");
// ... and now the main form
if (cartVarExists(cart, hgHubConnectCgiDestUrl))
destUrl = cartOptionalString(cart, hgHubConnectCgiDestUrl);
printf("<FORM ACTION=\"%s\" METHOD=\"POST\" NAME=\"mainForm\">\n", destUrl);
cartSaveSession(cart);
// we have two tabs for the public and unlisted hubs
printf("<div id=\"tabs\">"
"<ul> <li><a href=\"#publicHubs\">Public Hubs</a></li>"
"<li><a href=\"#unlistedHubs\">My Hubs</a></li> "
"</ul> ");
struct hash *publicHash = hgHubConnectPublic();
hgHubConnectUnlisted(hubList, publicHash);
printf("</div>");
printf("<div class=\"tabFooter\">");
cgiMakeButton("Submit", "Use Selected Hubs");
char *emailAddress = cfgOptionDefault("hub.emailAddress","*****@*****.**");
printf("<span class=\"small\">"
"Contact <A HREF=\"mailto:%s\">%s</A> to add a public hub."
"</span>\n", emailAddress,emailAddress);
printf("</div>");
cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on");
printf("</div>\n");
puts("</FORM>");
cartWebEnd();
}
void wikiPlot()
/* wikiPlot - Quick plots of maps vs. each other. */
{
boolean gotDir = cgiVarExists("contigDir");
double step;
contigDir = cgiUsualString("contigDir", contigDir);
mapX = cgiUsualString("mapX", mapX);
mapY = cgiUsualString("mapY", mapY);
pix = cgiUsualInt("pix", pix);
xOff = cgiUsualDouble("xOff", xOff);
yOff = cgiUsualDouble("yOff", yOff);
zoom = cgiUsualDouble("zoom", zoom);
step = 0.1 * 1/zoom;
if (cgiVarExists("boxOut"))
{
double invZoom = 1.0/zoom;
double xCen = xOff + invZoom*0.5;
double yCen = yOff + invZoom*0.5;
zoom /= 2;
invZoom = 1.0/zoom;
xOff = xCen - invZoom*0.5;
yOff = yCen - invZoom*0.5;
}
else if (cgiVarExists("boxUp"))
yOff -= step;
else if (cgiVarExists("boxDown"))
yOff += step;
else if (cgiVarExists("boxLeft"))
xOff -= step;
else if (cgiVarExists("boxRight"))
xOff += step;
else if (cgiVarExists("boxUpLeft"))
{
yOff -= step;
xOff -= step;
}
else if (cgiVarExists("boxUpRight"))
{
yOff -= step;
xOff += step;
}
else if (cgiVarExists("boxDownLeft"))
{
yOff += step;
xOff -= step;
}
else if (cgiVarExists("boxDownRight"))
{
yOff += step;
xOff += step;
}
else if (cgiVarExists("unzoom"))
{
xOff = yOff = -0.05;
zoom = 0.9;
}
printf("<FORM ACTION=\"../cgi-bin/wikiPlot\" METHOD=\"GET\">\n");
printf("<TABLE BORDER=0 WIDTH=\"100%%\">\n");
printf("<TR>\n");
printf("<TD WIDTH=\"78%%\">\n");
printf("<B>Wiki Plotter</B><BR>\n");
printf("<B>Contig: </B>");
cgiMakeTextVar("contigDir", contigDir, 0);
if (gotDir)
{
cgiMakeButton("refresh", "refresh");
}
else
cgiMakeButton("submit", "submit");
printf("<BR>\n");
printf("<B>Map X: </B>");
cgiMakeTextVar("mapX", mapX, 12);
printf("<B>Map Y: </B>");
cgiMakeTextVar("mapY", mapY, 12);
printf("<B>Pixels: </B>");
cgiMakeIntVar("pix", pix, 4);
printf("</TD>\n");
printf("<TD WIDTH=\"22%%\">\n");
if (gotDir)
printBox();
printf("</TD>\n");
printf("</TR>\n");
printf("</TABLE>\n");
if (gotDir)
{
char xFile[512], yFile[512];
struct hash *xHash = NULL, *yHash = NULL;
struct clonePos *xList = NULL, *yList = NULL;
sprintf(xFile, "%s/%s", contigDir, mapX);
sprintf(yFile, "%s/%s", contigDir, mapY);
loadMaps(xFile, yFile, &xList, &yList, &xHash, &yHash);
makePlot(xList, yList, yHash);
}
/* Save hidden vars. */
{
char buf[256];
sprintf(buf, "%f", zoom);
cgiMakeHiddenVar("zoom", buf);
sprintf(buf, "%f", xOff);
cgiMakeHiddenVar("xOff", buf);
sprintf(buf, "%f", yOff);
cgiMakeHiddenVar("yOff", buf);
}
printf("</FORM>\n");
}
void mainPageAfterOpen(struct sqlConnection *conn)
/* Put up main page assuming htmlOpen()/htmlClose()
* will happen in calling routine. */
{
hPrintf("%s",
"Use this program to retrieve the data associated with a track in text "
"format, to calculate intersections between tracks, and to retrieve "
"DNA sequence covered by a track. For help in using this application "
"see <A HREF=\"#Help\">Using the Table Browser</A> for a description "
"of the controls in this form, the "
"<A HREF=\"../goldenPath/help/hgTablesHelp.html\">User's Guide</A> for "
"general information and sample queries, and the OpenHelix Table Browser "
"<A HREF=\"http://www.openhelix.com/cgi/tutorialInfo.cgi?id=28\" "
"TARGET=_blank>tutorial</A> for a narrated presentation of the software "
"features and usage. "
"For more complex queries, you may want to use "
"<A HREF=\""GALAXY_URL_BASE"\" target=_BLANK>Galaxy</A> or "
"our <A HREF=\"../goldenPath/help/mysql.html\">public "
"MySQL server</A>. "
"To examine the biological function of your set through annotation "
"enrichments, send the data to "
"<A HREF=\"http://great.stanford.edu\">GREAT</A>. Refer to the "
"<A HREF=\"../goldenPath/credits.html\">Credits</A> page for the list of "
"contributors and usage restrictions associated with these data. "
"All tables can be downloaded in their entirety from the "
"<A HREF=\"http://hgdownload.cse.ucsc.edu/downloads.html\""
">Sequence and Annotation Downloads</A> page."
);
hPrintf("<script type=\"text/javascript\">\n");
hPrintf("function onSelectGreat() {\n");
hPrintf("document.getElementById('checkboxGalaxy').checked=false;\n");
hPrintf("document.getElementById('outBed').selected=true;\n");
hPrintf("return true;\n");
hPrintf("}\n");
hPrintf("</script>\n");
/* Main form. */
hPrintf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=%s>\n",
getScriptName(), cartUsualString(cart, "formMethod", "POST"));
cartSaveSession(cart);
jsWriteFunctions();
showMainControlTable(conn);
hPrintf("</FORM>\n");
/* Hidden form - for benefit of javascript. */
{
static char *saveVars[] = {
"clade", "org", "db", hgtaGroup, hgtaTrack, hgtaTable, hgtaRegionType,
hgtaRange, hgtaOutputType, hgtaOutFileName};
jsCreateHiddenForm(cart, getScriptName(), saveVars, ArraySize(saveVars));
}
/* Hidden form for jumping to custom tracks CGI. */
hPrintf("<FORM ACTION='%s' NAME='customTrackForm'>", hgCustomName());
cartSaveSession(cart);
hPrintf("</FORM>\n");
/* Hidden form for jumping to track hub manager CGI. */
hPrintf("<FORM ACTION='%s' NAME='trackHubForm'>", hgHubConnectName());
cgiMakeHiddenVar(hgHubConnectCgiDestUrl, "../cgi-bin/hgTables");
cartSaveSession(cart);
hPrintf("</FORM>\n");
webNewSection("<A NAME=\"Help\"></A>Using the Table Browser\n");
printMainHelp();
}
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>");
}
static void trackConfig(struct track *trackList, struct group *groupList,
char *groupTarget, int changeVis)
/* Put up track configurations. If groupTarget is
* NULL then set visibility for tracks in all groups. Otherwise,
* just set it for the given group. If vis is -2, then visibility is
* unchanged. If -1 then set visibility to default, otherwise it should
* be tvHide, tvDense, etc. */
{
struct group *group;
boolean showedRuler = FALSE;
setRulerMode();
changeTrackVis(groupList, groupTarget, changeVis);
/* Set up ruler mode according to changeVis. */
#ifdef BOB_DOESNT_LIKE
if (changeVis != -2)
{
if (groupTarget == NULL ||
(groupList != NULL && sameString(groupTarget, groupList->name)))
{
if (changeVis == -1)
rulerMode = tvFull;
else
rulerMode = changeVis;
}
}
#endif /* BOB_DOESNT_LIKE */
jsInit();
cgiMakeHiddenVar(configGroupTarget, "none");
// Now all groups are in a single table, divided by an empty borderless row
hPrintf("<TABLE BORDER='0' CELLSPACING='0' class='groupLists'>\n");
for (group = groupList; group != NULL; group = group->next)
{
struct trackRef *tr;
if (group->trackList == NULL)
continue;
/* check if group section should be displayed */
char *otherState;
char *indicator;
char *indicatorImg;
boolean isOpen = !isCollapsedGroup(group);
collapseGroupGoodies(isOpen, FALSE, &indicatorImg,
&indicator, &otherState);
hPrintf("<TR NOWRAP class='blueToggleBar'>");
hPrintf("<TH NOWRAP align='left' colspan=3>");
hPrintf("<table style='width:100%%;'><tr class='noData'><td style='text-align:left;'>");
hPrintf("\n<A NAME='%sGroup'></A>",group->name);
hPrintf("<input type=hidden name='%s' id='%s' value=%d>",
collapseGroupVar(group->name),collapseGroupVar(group->name), (isOpen?0:1));
char idText[256];
safef(idText, sizeof idText, "%s_button", group->name);
hPrintf("<IMG class='toggleButton' "
"id='%s' src='%s' alt='%s' title='%s this group'> ",
idText, indicatorImg, indicator,isOpen?"Collapse":"Expand");
// TODO XSS filter group->name
jsOnEventByIdF("click", idText, "return vis.toggleForGroup(this,'%s');", group->name);
hPrintf("<B> %s</B> ", group->label);
hPrintf(" ");
hPrintf("</td><td style='text-align:right;'>\n");
safef(idText, sizeof idText, "%s_hideAllBut", group->name);
hPrintf("<INPUT TYPE=SUBMIT NAME=\"%s\" id='%s' VALUE=\"%s\" "
"title='Hide all tracks in this groups'>",
configHideAll, idText, "hide all");
// TODO XSS filter configGroupTarget
char jsText[256];
// used several times
safef(jsText, sizeof jsText, "document.mainForm.%s.value='%s'; %s",
configGroupTarget, group->name, jsSetVerticalPosition("mainForm"));
jsOnEventById("click", idText, jsText);
hPrintf(" ");
safef(idText, sizeof idText, "%s_showAllBut", group->name);
hPrintf("<INPUT TYPE=SUBMIT NAME=\"%s\" id='%s' VALUE=\"%s\" "
"title='Show all tracks in this groups'>",
configShowAll, idText, "show all");
jsOnEventById("click", idText, jsText);
hPrintf(" ");
safef(idText, sizeof idText, "%s_defaultBut", group->name);
hPrintf("<INPUT TYPE=SUBMIT NAME=\"%s\" id='%s' VALUE=\"%s\" "
"title='Show default tracks in this group'>",
configDefaultAll, idText, "default");
jsOnEventById("click", idText, jsText);
hPrintf(" ");
/* do not want all the submit buttons named the same. It is
* confusing to the javascript submit() function.
*/
char submitName[256];
safef(submitName, sizeof(submitName), "%sSubmit", group->name);
cgiMakeButtonWithMsg(submitName, "submit","Submit your selections and view them in the browser");
hPrintf("</td></tr></table>\n");
hPrintf("</TH></TR>\n");
/* First non-CT, non-hub group gets ruler. */
if (!showedRuler && !isHubTrack(group->name) &&
differentString(group->name, "user"))
{
showedRuler = TRUE;
hPrintf("<TR %sid='%s-0'>",(isOpen ? "" : "style='display: none'"), group->name);
hPrintf("<TD>");
hPrintf("<A HREF=\"%s?%s=%s&c=%s&g=%s&hgTracksConfigPage=configure\">", hgTrackUiName(),
cartSessionVarName(), cartSessionId(cart),
chromName, RULER_TRACK_NAME);
hPrintf("%s</A>", RULER_TRACK_LABEL);
hPrintf("</TD><TD>");
hTvDropDownClass("ruler", rulerMode, FALSE, rulerMode ? "normalText" : "hiddenText");
hPrintf("</TD><TD>");
hPrintf("Chromosome position in bases. (Clicks here zoom in 3x)");
hPrintf("</TD></TR>\n");
}
/* Scan track list to determine which supertracks have visible member
* tracks, and to insert a track in the list for the supertrack.
* Sort tracks and supertracks together by priority */
makeGlobalTrackHash(trackList);
groupTrackListAddSuper(cart, group);
if (!withPriorityOverride)
{
/* sort hierarchically by priority, considering supertracks */
struct trackRef *refList = NULL, *ref;
for (tr = group->trackList; tr != NULL; tr = tr->next)
{
struct track *track = tr->track;
if (tdbIsSuperTrackChild(track->tdb))
/* ignore supertrack member tracks till supertrack is found */
continue;
AllocVar(ref);
ref->track = track;
slAddTail(&refList, ref);
if (tdbIsSuper(track->tdb))
{
struct slRef *child = track->tdb->children;
for (; child != NULL; child=child->next)
{
struct trackDb *childTdb = child->val;
struct track *childTrack = hashFindVal(trackHash, childTdb->track);
// Try adding downloadsOnly track
if (childTrack == NULL && tdbIsDownloadsOnly(childTdb))
{
AllocVar(childTrack); // Fake a track!
childTrack->tdb = childTdb;
childTrack->hasUi = FALSE;
}
if (childTrack != NULL)
{
AllocVar(ref);
ref->track = childTrack;
slAddTail(&refList, ref);
}
}
}
}
group->trackList = refList;
}
/* Loop through this group and display */
int rowCount=1;
for (tr = group->trackList; tr != NULL; tr = tr->next)
{
struct track *track = tr->track;
struct trackDb *tdb = track->tdb;
hPrintf("<TR %sid='%s-%d'>",(isOpen ? "" : "style='display: none;'"),
group->name, rowCount++);
hPrintf("<TD NOWRAP>");
if (tdbIsSuperTrackChild(tdb))
/* indent members of a supertrack */
hPrintf(" ");
// Print an icon before the title when one is defined
hPrintPennantIcon(tdb);
if (track->hasUi)
hPrintf("<A TITLE='%s%s...' HREF='%s?%s=%s&g=%s&hgTracksConfigPage=configure'>",
tdb->parent ? "Part of super track: " : "Configure ",
tdb->parent ? tdb->parent->shortLabel : tdb->shortLabel,
hTrackUiForTrack(tdb->track),
cartSessionVarName(), cartSessionId(cart), track->track);
hPrintf(" %s", tdb->shortLabel);
if (tdbIsSuper(tdb))
hPrintf("...");
if (track->hasUi)
hPrintf("</A>");
hPrintf("</TD><TD NOWRAP>");
if (tdbIsSuperTrackChild(tdb))
/* indent members of a supertrack */
hPrintf(" ");
/* If track is not on this chrom print an informational
message for the user. */
if (tdbIsDownloadsOnly(tdb)) // No vis display for downloadsOnly
hPrintf("<A TITLE='Downloadable files...' HREF='%s?%s=%s&g=%s'>Downloads</A>",
hgFileUiName(),cartSessionVarName(), cartSessionId(cart), tdb->track);
else if (hTrackOnChrom(track->tdb, chromName))
{
if (tdbIsSuper(track->tdb))
{
/* supertrack dropdown is hide/show */
superTrackDropDown(cart, track->tdb, 1);
}
else
{
/* check for option of limiting visibility to one mode */
hTvDropDownClassVisOnly(track->track, track->visibility,
rTdbTreeCanPack(track->tdb),
(track->visibility == tvHide) ? "hiddenText" : "normalText",
trackDbSetting(track->tdb, "onlyVisibility"));
}
}
else
hPrintf("[No data-%s]", chromName);
hPrintf("</TD><TD NOWRAP>");
hPrintf("%s", tdb->longLabel);
hPrintf("</TD></TR>\n");
}
hPrintf("<tr class='noData'><td colspan=3>");
cgiDown(0.9);
hPrintf("</td></tr>\n");
}
hPrintf("</TABLE>\n");
}
void monitorSubmission(struct sqlConnection *conn)
/* Write out information about submission. */
{
char *url = trimSpaces(cgiString("url"));
cgiMakeHiddenVar("url", url);
struct edwSubmit *sub = edwMostRecentSubmission(conn, url);
time_t startTime = 0, endTime = 0, endUploadTime = 0;
if (sub == NULL)
{
int posInQueue = edwSubmitPositionInQueue(conn, url, NULL);
if (posInQueue == 0)
printf("%s is first in the submission queue, but upload has not started<BR>\n", url);
else if (posInQueue > 0)
printf("%s is in submission queue with %d submissions ahead of it<BR>\n", url, posInQueue);
else
{
printf("%s status unknown.", url);
}
}
else
{
startTime = sub->startUploadTime;
endUploadTime = sub->endUploadTime;
endTime = (endUploadTime ? endUploadTime : edwNow());
int timeSpan = endTime - startTime;
long long thisUploadSize = sub->byteCount - sub->oldBytes;
long long curSize = 0; // Amount of current file we know we've transferred.
/* Print title letting them know if upload is done or in progress. */
printf("<B>Submission by %s is ", userEmail);
if (!isEmpty(sub->errorMessage))
{
if (endUploadTime == 0)
printf("having problems...");
else
printf("stopped by uploader request.");
}
else if (endUploadTime != 0)
{
printf("uploaded.");
}
else
printf("in progress...");
printf("</B><BR>\n");
/* Print URL and how far along we are at the file level. */
if (!isEmpty(sub->errorMessage))
{
printf("<B>error:</B> %s<BR>\n", sub->errorMessage);
cgiMakeButton("getUrl", "try submission again");
printf("<BR>");
}
printf("<B>url:</B> %s<BR>\n", sub->url);
printf("<B>files count:</B> %d<BR>\n", sub->fileCount);
if (sub->oldFiles > 0)
printf("<B>files already in warehouse:</B> %u<BR>\n", sub->oldFiles);
if (sub->metaChangeCount > 0)
printf("<B>old files with new tags in this submission</B> %d<BR>", sub->metaChangeCount);
if (sub->oldFiles != sub->fileCount)
{
printf("<B>files transferred:</B> %u<BR>\n", sub->newFiles);
printf("<B>files remaining:</B> %u<BR>\n", sub->fileCount - sub->oldFiles - sub->newFiles);
}
/* Report validation status */
printf("<B>new files validated:</B> %u of %u<BR>\n", edwSubmitCountNewValid(sub, conn),
sub->newFiles);
/* Print error message, and in case of error skip file-in-transfer info. */
if (isEmpty(sub->errorMessage))
{
/* If possible print information about file en route */
if (endUploadTime == 0)
{
struct edwFile *ef = edwFileInProgress(conn, sub->id);
if (ef != NULL)
{
char path[PATH_LEN];
safef(path, sizeof(path), "%s%s", edwRootDir, ef->edwFileName);
if (ef->endUploadTime > 0)
curSize = ef->size;
else
curSize = paraFetchedSoFar(path);
printf("<B>file in route:</B> %s", ef->submitFileName);
printf(" (%d%% transferred)<BR>\n", (int)(100.0 * curSize / ef->size));
}
}
}
/* Report bytes transferred */
long long transferredThisTime = curSize + sub->newBytes;
printf("<B>total bytes transferred:</B> ");
long long totalTransferred = transferredThisTime + sub->oldBytes;
printLongWithCommas(stdout, totalTransferred);
printf(" of ");
printLongWithCommas(stdout, sub->byteCount);
if (sub->byteCount != 0)
printf(" (%d%%)<BR>\n", (int)(100.0 * totalTransferred / sub->byteCount));
else
printf("<BR>\n");
/* Report transfer speed if possible */
if (isEmpty(sub->errorMessage))
{
if (timeSpan > 0)
{
printf("<B>transfer speed:</B> ");
printLongWithCommas(stdout, (curSize + sub->newBytes)/timeSpan);
printf(" bytes/sec<BR>\n");
}
/* Report start time and duration */
printf("<B>submission started:</B> %s<BR>\n", ctime(&startTime));
struct dyString *duration = edwFormatDuration(timeSpan);
/* Try and give them an ETA if we aren't finished */
if (endUploadTime == 0 && timeSpan > 0)
{
printf("<B>time so far:</B> %s<BR>\n", duration->string);
double bytesPerSecond = (double)transferredThisTime/timeSpan;
long long bytesRemaining = thisUploadSize - curSize - sub->newBytes;
if (bytesPerSecond > 0)
{
long long estimatedFinish = bytesRemaining/bytesPerSecond;
struct dyString *eta = edwFormatDuration(estimatedFinish);
printf("<B>estimated finish in:</B> %s<BR>\n", eta->string);
}
}
else
{
printf("<B>submission time:</B> %s<BR>\n", duration->string);
cgiMakeButton("getUrl", "submit another data set");
}
}
}
cgiMakeButton("monitor", "refresh status");
if (endUploadTime == 0 && isEmpty(sub->errorMessage))
cgiMakeButton(stopButtonName, "stop upload");
printf(" <input type=\"button\" value=\"browse submissions\" "
"onclick=\"window.location.href='edwWebBrowse';\">\n");
edwPrintLogOutButton();
}
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());
}
void doSearchTracks(struct group *groupList)
{
webIncludeResourceFile("ui.dropdownchecklist.css");
jsIncludeFile("ui.dropdownchecklist.js",NULL);
// This line is needed to get the multi-selects initialized
jsIncludeFile("ddcl.js",NULL);
struct group *group;
char *groups[128];
char *labels[128];
int numGroups = 1;
groups[0] = ANYLABEL;
labels[0] = ANYLABEL;
char *nameSearch = cartOptionalString(cart, TRACK_SEARCH_ON_NAME);
char *typeSearch = cartUsualString( cart, TRACK_SEARCH_ON_TYPE,ANYLABEL);
char *simpleEntry = cartOptionalString(cart, TRACK_SEARCH_SIMPLE);
char *descSearch = cartOptionalString(cart, TRACK_SEARCH_ON_DESCR);
char *groupSearch = cartUsualString( cart, TRACK_SEARCH_ON_GROUP,ANYLABEL);
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 tracksFound = 0;
boolean searchTermsExist = FALSE;
int cols;
char buf[512];
char *currentTab = cartUsualString(cart, TRACK_SEARCH_CURRENT_TAB, "simpleTab");
enum searchTab selectedTab = (sameString(currentTab, "advancedTab") ? advancedTab : simpleTab);
// NOTE: could support quotes in simple tab by detecting quotes and choosing
// to use doesNameMatch() || doesDescriptionMatch()
if (selectedTab == simpleTab && !isEmpty(simpleEntry))
stripChar(simpleEntry, '"');
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.
// Subtrack settings must be removed when composite/view settings are updated
parentChildCartCleanup(trackList,cart,oldVars);
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 id='simpleTable' 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='findTracks.searchButtonsEnable(true);'>\n",
TRACK_SEARCH_SIMPLE,simpleEntry == NULL ? "" : simpleEntry);
if (selectedTab==simpleTab && simpleEntry)
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='findTracks.clear();'>\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 id='advancedTable' 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='findTracks.searchButtonsEnable(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='findTracks.searchButtonsEnable(true);' "
"style='max-width:536px; width:536px; font-size:.9em;'>",
TRACK_SEARCH_ON_DESCR, descSearch == NULL ? "" : descSearch);
hPrintf("</td></tr>\n");
if (selectedTab==advancedTab && !isEmpty(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 (selectedTab==advancedTab && !isEmpty(groupSearch) && !sameString(groupSearch,ANYLABEL))
searchTermsExist = TRUE;
// 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 (selectedTab==advancedTab && !isEmpty(typeSearch) && !sameString(typeSearch,ANYLABEL))
searchTermsExist = TRUE;
// mdb selects
struct slPair *mdbSelects = NULL;
if (metaDbExists)
{
struct slPair *mdbVars = mdbVarsSearchable(conn,TRUE,FALSE); // Tables but not file only objects
mdbSelects = mdbSelectPairs(cart, mdbVars);
char *output = mdbSelectsHtmlRows(conn,mdbSelects,mdbVars,cols,FALSE); // not a fileSearch
if (output)
{
puts(output);
freeMem(output);
}
slPairFreeList(&mdbVars);
}
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='findTracks.clear();'>\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");
hPrintf("</div>\n");
hPrintf("</form>\n");
hPrintf("</div>"); // Restricts to max-width:1000px;
cgiDown(0.8);
if (measureTiming)
measureTime("Rendered tabs");
if (doSearch)
{
// Now search
struct slRef *tracks = NULL;
if (selectedTab==simpleTab && !isEmpty(simpleEntry))
tracks = simpleSearchForTracksstruct(simpleEntry);
else if (selectedTab==advancedTab)
tracks = advancedSearchForTracks(conn,groupList,nameSearch,typeSearch,descSearch,
groupSearch,mdbSelects);
if (measureTiming)
measureTime("Searched for tracks");
// Sort and Print results
if (selectedTab!=filesTab)
{
enum sortBy sortBy = cartUsualInt(cart,TRACK_SEARCH_SORT,sbRelevance);
tracksFound = slCount(tracks);
if (tracksFound > 1)
findTracksSort(&tracks,sortBy);
displayFoundTracks(cart,tracks,tracksFound,sortBy);
if (measureTiming)
measureTime("Displayed found tracks");
}
slPairFreeList(&mdbSelects);
}
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();
}
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();
}
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();
}
static void trackConfig(struct track *trackList, struct group *groupList,
char *groupTarget, int changeVis)
/* Put up track configurations. If groupTarget is
* NULL then set visibility for tracks in all groups. Otherwise,
* just set it for the given group. If vis is -2, then visibility is
* unchanged. If -1 then set visibility to default, otherwise it should
* be tvHide, tvDense, etc. */
{
#ifdef PRIORITY_CHANGES_IN_CONFIG_UI
char pname[512];
char gname[512];
#endif///def PRIORITY_CHANGES_IN_CONFIG_UI
struct group *group;
boolean showedRuler = FALSE;
setRulerMode();
changeTrackVis(groupList, groupTarget, changeVis);
/* Set up ruler mode according to changeVis. */
#ifdef BOB_DOESNT_LIKE
if (changeVis != -2)
{
if (groupTarget == NULL ||
(groupList != NULL && sameString(groupTarget, groupList->name)))
{
if (changeVis == -1)
rulerMode = tvFull;
else
rulerMode = changeVis;
}
}
#endif /* BOB_DOESNT_LIKE */
jsInit();
cgiMakeHiddenVar(configGroupTarget, "none");
boolean isFirstNotCtGroup = TRUE;
for (group = groupList; group != NULL; group = group->next)
{
struct trackRef *tr;
if (group->trackList == NULL)
continue;
/* check if group section should be displayed */
char *otherState;
char *indicator;
char *indicatorImg;
boolean isOpen = !isCollapsedGroup(group);
collapseGroupGoodies(isOpen, FALSE, &indicatorImg,
&indicator, &otherState);
hTableStart();
hPrintf("<TR NOWRAP>");
hPrintf("<TH NOWRAP align=\"left\" colspan=3 BGCOLOR=#536ED3>");
hPrintf("\n<A NAME='%sGroup'></A>",group->name);
hPrintf("<input type=hidden name='%s' id='%s' value=%d>",
collapseGroupVar(group->name),collapseGroupVar(group->name), (isOpen?0:1));
hPrintf("<A HREF='%s?%s&%s=%s#%sGroup' class='bigBlue'><IMG height=22 width=22 onclick=\"return toggleTrackGroupVisibility(this,'%s');\" id='%s_button' src='%s' alt='%s' class='bigBlue' title='%s this group'></A> ",
hgTracksName(), cartSidUrlString(cart),collapseGroupVar(group->name),
otherState, group->name, group->name, group->name, indicatorImg, indicator,isOpen?"Collapse":"Expand");
hPrintf("<B> %s</B> ", wrapWhiteFont(group->label));
hPrintf(" ");
hPrintf("<INPUT TYPE=SUBMIT NAME=\"%s\" VALUE=\"%s\" "
"onClick=\"document.mainForm.%s.value='%s'; %s\" title='Hide all tracks in this groups'>",
configHideAll, "hide all", configGroupTarget, group->name,
jsSetVerticalPosition("mainForm"));
hPrintf(" ");
hPrintf("<INPUT TYPE=SUBMIT NAME=\"%s\" VALUE=\"%s\" "
"onClick=\"document.mainForm.%s.value='%s'; %s\" title='Show all tracks in this groups'>",
configShowAll, "show all", configGroupTarget, group->name,
jsSetVerticalPosition("mainForm"));
hPrintf(" ");
hPrintf("<INPUT TYPE=SUBMIT NAME=\"%s\" VALUE=\"%s\" "
"onClick=\"document.mainForm.%s.value='%s'; %s\" title='Show default tracks in this group'>",
configDefaultAll, "default", configGroupTarget, group->name,
jsSetVerticalPosition("mainForm"));
hPrintf(" ");
/* do not want all the submit buttons named the same. It is
* confusing to the javascript submit() function.
*/
char submitName[256];
safef(submitName, sizeof(submitName), "%sSubmit", group->name);
cgiMakeButtonWithMsg(submitName, "submit","Submit your selections and view them in the browser");
#ifdef PRIORITY_CHANGES_IN_CONFIG_UI
if (withPriorityOverride)
{
hPrintf(" ");
hPrintf(" ");
hPrintf(" ");
hPrintf("%s", wrapWhiteFont("Group Order: "));
}
#endif///def PRIORITY_CHANGES_IN_CONFIG_UI
hPrintf("</TH>\n");
#ifdef PRIORITY_CHANGES_IN_CONFIG_UI
if (withPriorityOverride)
{
hPrintf("<TH>\n");
safef(pname, sizeof(pname), "%s.priority",group->name);
hDoubleVar(pname, (double)group->priority, 4);
hPrintf("</TH>\n");
if (isOpen)
hPrintf("<TH align=CENTER BGCOLOR=#536ED3><B> %s</B></TH> ", wrapWhiteFont("Group"));
hPrintf("\n");
}
#endif///def PRIORITY_CHANGES_IN_CONFIG_UI
hPrintf("</TR>\n");
/* First non-CT group gets ruler. */
if (!showedRuler && isFirstNotCtGroup &&
differentString(group->name, "user"))
{
showedRuler = TRUE;
hPrintf("<TR %sid='%s-0'>",(isOpen ? "" : "style='display: none'"), group->name);
hPrintf("<TD>");
hPrintf("<A HREF=\"%s?%s=%u&c=%s&g=%s&hgTracksConfigPage=configure\">", hgTrackUiName(),
cartSessionVarName(), cartSessionId(cart),
chromName, RULER_TRACK_NAME);
hPrintf("%s</A>", RULER_TRACK_LABEL);
hPrintf("</TD>");
hPrintf("<TD>");
hTvDropDownClass("ruler", rulerMode, FALSE, rulerMode ? "normalText" : "hiddenText");
hPrintf("</TD>");
hPrintf("<TD>");
hPrintf("Chromosome position in bases. (Clicks here zoom in 3x)");
hPrintf("</TD>");
#ifdef PRIORITY_CHANGES_IN_CONFIG_UI
if (withPriorityOverride)
{
hPrintf("<TD>");
hPrintf("</TD>");
hPrintf("<TD>");
hPrintf("</TD>");
}
#endif///def PRIORITY_CHANGES_IN_CONFIG_UI
hPrintf("</TR>\n");
}
if (differentString(group->name, "user"))
isFirstNotCtGroup = FALSE;
/* Scan track list to determine which supertracks have visible member
* tracks, and to insert a track in the list for the supertrack.
* Sort tracks and supertracks together by priority */
groupTrackListAddSuper(cart, group);
if (!withPriorityOverride)
{
/* sort hierarchically by priority, considering supertracks */
struct trackRef *refList = NULL, *ref;
for (tr = group->trackList; tr != NULL; tr = tr->next)
{
struct track *track = tr->track;
if (tdbIsSuperTrackChild(track->tdb))
/* ignore supertrack member tracks till supertrack is found */
continue;
AllocVar(ref);
ref->track = track;
slAddTail(&refList, ref);
if (tdbIsSuper(track->tdb))
{
struct trackRef *tr2;
for (tr2 = group->trackList; tr2 != NULL; tr2 = tr2->next)
{
char *parent = tr2->track->tdb->parentName;
if (parent && sameString(parent, track->track))
{
AllocVar(ref);
ref->track = tr2->track;
slAddTail(&refList, ref);
}
}
}
}
group->trackList = refList;
}
/* Loop through this group and display */
int rowCount=1;
for (tr = group->trackList; tr != NULL; tr = tr->next)
{
struct track *track = tr->track;
struct trackDb *tdb = track->tdb;
hPrintf("<TR %sid='%s-%d'>",(isOpen ? "" : "style='display: none'"),group->name, rowCount++);
hPrintf("<TD NOWRAP>");
if (tdbIsSuperTrackChild(tdb))
/* indent members of a supertrack */
hPrintf(" ");
// Print an icon before the title when one is defined
hPrintPennantIcon(track->tdb);
if (track->hasUi)
hPrintf("<A %s%s%s HREF=\"%s?%s=%u&g=%s&hgTracksConfigPage=configure\">",
tdb->parent ? "TITLE=\"Part of super track: " : "",
tdb->parent ? tdb->parent->shortLabel : "",
tdb->parent ? "...\"" : "", hgTrackUiName(),
cartSessionVarName(), cartSessionId(cart), track->track);
hPrintf(" %s", track->shortLabel);
if (tdbIsSuper(track->tdb))
hPrintf("...");
if (track->hasUi)
hPrintf("</A>");
hPrintf("</TD>");
hPrintf("<TD NOWRAP>");
if (tdbIsSuperTrackChild(tdb))
/* indent members of a supertrack */
hPrintf(" ");
/* If track is not on this chrom print an informational
message for the user. */
if (hTrackOnChrom(track->tdb, chromName))
{
if (tdbIsSuper(track->tdb))
{
/* supertrack dropdown is hide/show */
superTrackDropDown(cart, track->tdb, 1);
}
else
{
/* check for option of limiting visibility to one mode */
hTvDropDownClassVisOnly(track->track, track->visibility,
track->canPack, (track->visibility == tvHide) ?
"hiddenText" : "normalText",
trackDbSetting(track->tdb, "onlyVisibility"));
}
}
else
hPrintf("[No data-%s]", chromName);
hPrintf("</TD>");
hPrintf("<TD NOWRAP>");
hPrintf("%s", track->longLabel);
hPrintf("</TD>");
#ifdef PRIORITY_CHANGES_IN_CONFIG_UI
if (withPriorityOverride)
{
hPrintf("<TD>");
safef(pname, sizeof(pname), "%s.priority",track->track);
hDoubleVar(pname, (double)track->priority, 4);
hPrintf("</TD>");
hPrintf("<TD>\n");
/* suppress group pull-down for supertrack members */
if (tdbIsSuperTrackChild(track->tdb))
hPrintf(" ");
else
{
safef(gname, sizeof(gname), "%s.group",track->track);
printGroupListHtml(gname, groupList, track->groupName);
}
hPrintf("</TD>");
}
#endif///def PRIORITY_CHANGES_IN_CONFIG_UI
hPrintf("</TR>\n");
}
hTableEnd();
hPrintf("<BR>");
}
}
