static struct customTrack *beginCustomTrack(char *table, int fields,
boolean doCt, boolean doWigHdr, boolean doDataPoints)
/* If doCt, return a new custom track object from TB cart settings and params;
* if !doCt, return NULL but print out a header line. */
{
char *ctName = cgiUsualString(hgtaCtName, table);
char *ctDesc = cgiUsualString(hgtaCtDesc, table);
char *ctUrl = cgiUsualString(hgtaCtUrl, "");
char *ctVis = cgiUsualString(hgtaCtVis, "dense");
int visNum = (int) hTvFromStringNoAbort(ctVis);
struct customTrack *ctNew = NULL;
if (visNum < 0)
visNum = 0;
if (doCt)
{
ctNew = newCt(ctName, ctDesc, visNum, ctUrl, fields);
if (doDataPoints)
{
struct dyString *wigSettings = newDyString(0);
struct tempName tn;
trashDirFile(&tn, "ct", hgtaCtTempNamePrefix, ".wib");
ctNew->wibFile = cloneString(tn.forCgi);
char *wiggleFile = cloneString(ctNew->wibFile);
chopSuffix(wiggleFile);
strcat(wiggleFile, ".wia");
ctNew->wigAscii = cloneString(wiggleFile);
chopSuffix(wiggleFile);
/* .wig file will be created upon encoding in customFactory */
/*strcat(wiggleFile, ".wig");
ctNew->wigFile = cloneString(wiggleFile);
*/
ctNew->wiggle = TRUE;
dyStringPrintf(wigSettings,
"type wiggle_0\nwibFile %s\n", ctNew->wibFile);
ctNew->tdb->settings = dyStringCannibalize(&wigSettings);
freeMem(wiggleFile);
}
}
else
{
if (doWigHdr)
hPrintf("track type=wiggle_0 name=\"%s\" description=\"%s\" "
"visibility=%d url=%s \n",
ctName, ctDesc, visNum, ctUrl);
else
hPrintf("track name=\"%s\" description=\"%s\" visibility=%d url=%s \n",
ctName, ctDesc, visNum, ctUrl);
}
return ctNew;
}
int main(int argc, char *argv[])
/* Process command line. */
{
cgiSpoof(&argc, argv);
textField = cgiUsualString("textField", textField);
fileComment = cgiUsualString("comment", fileComment);
picky = cgiBoolean("picky");
makeMain = cgiBoolean("main");
positiveOnly = cgiBoolean("positive");
if (argc != 3)
usage();
autoXml(argv[1], argv[2]);
return 0;
}
void doPlots()
/* Do all the plots. */
{
struct dyString *script = newDyString(2048);
struct dyString *dummy = newDyString(256);
char *skipPSet = cgiUsualString("skipPName", "G7153846@J939317_RC@j_at");
html = newDyString(1024);
hSetDb("mm5");
dyStringPrintf(script, "%s", rHeader);
/* Call query once to initialize altEvent. */
constructQueryForEvent(dummy, skipPSet, "dummy");
assert(altEvent);
fprintf(stdout, "<h3>Plots for %s (%s)</h3>\n", altEvent->geneName, skipPSet);
fflush(stdout);
/* Probe set plots. */
doRegressionPlot(script, skipPSet,
"mouseAEvent_inc_intensity",
"mouseAEvent_skip_intensity",
"mouseAEvent_gene_prob");
doProbeSet(script, skipPSet);
doProbeSetPVals(script, skipPSet);
doNormProbes(script, skipPSet);
fflush(stdout);
fflush(stderr);
invokeR(script);
fputs(html->string, stdout);
}
static void choiceMenu()
/* Put up choice menu. */
{
static char *choices[] = {"one", "two", "three"};
char *var = "num";
char *val = cgiUsualString(var, "two");
char *script = "onchange=\""
" document.mainForm.submit();\"";
cgiMakeDropListFull(var, choices, choices, ArraySize(choices), val, script);
}
int main(int argc, char *argv[])
{
cgiSpoof(&argc, argv);
if(argc == 1)
usage();
else
{
suffix = cgiUsualString("suffix", "pairs.sample.norm");
doAll = cgiBoolean("doAll");
avgTranscriptomeExps();
}
return 0;
}
void doAnalysisForBed(struct bed *bed)
{
char *hgdbTestTable = cgiUsualString("hgdbTestTable","affyTrans_hg12");
char *hgdbTestName = "sugnet";
FILE *tmpFile = NULL;
char commandBuffer[4096];
char *fileNameRoot = getFileNameForBed(bed);
char bedFile[512];
char dataFile[512];
int retVal = 0;
/* Print out bed. */
safef(bedFile, sizeof(bedFile), "%s.bed", fileNameRoot);
tmpFile = mustOpen(bedFile, "w");
bedTabOutN(bed, 12, tmpFile);
carefulClose(&tmpFile);
/* Get samples for bed. */
safef(dataFile, sizeof(dataFile), "%s.data", fileNameRoot);
safef(commandBuffer, sizeof(commandBuffer), "samplesForCoordinates bedFile=%s hgdbTestName=%s hgdbTestTable=%s > %s",
bedFile, hgdbTestName, hgdbTestTable, dataFile);
retVal = system(commandBuffer);
if(retVal != 0)
{
warn("%s failed running command:\n%s", fileNameRoot, commandBuffer);
return;
}
safef(commandBuffer, sizeof(commandBuffer), "cp %s tmp.data", dataFile);
retVal = system(commandBuffer);
/* Run R analysis on data file. */
warn("Running R for %s", fileNameRoot);
fflush(stderr);
safef(commandBuffer, sizeof(commandBuffer), "R --vanilla < /cluster/home/sugnet/sugnet/R/maReg/R/runAnalysis.R");
warn("Done with R");
fflush(stderr);
retVal = system(commandBuffer);
if(retVal != 0)
{
warn("%s failed running command:\n%s", fileNameRoot, commandBuffer);
return;
}
bedsAnalyzed++;
}
int main(int argc, char *argv[])
/* Process command line. */
{
long enteredMainTime = clock1000();
struct dyString *headText = newDyString(512);
char *destination = cgiUsualString("destination", defaultDestination);
if (strstr(destination, "://"))
errAbort("To stop Open Redirect abuse, only relative URLs are supported. "
"Request for destination=[%s] rejected.\n", destination);
dyStringPrintf(headText,
"<META HTTP-EQUIV=\"REFRESH\" CONTENT=\"0;URL=%s\">"
"<META HTTP-EQUIV=\"Pragma\" CONTENT=\"no-cache\">"
"<META HTTP-EQUIV=\"Expires\" CONTENT=\"-1\">"
,destination);
htmShellWithHead("Reset Cart", headText->string, doMiddle, NULL);
dyStringFree(&headText);
cgiExitTime("cartReset", enteredMainTime);
return 0;
}
/** load the sage experiment data
*/
struct sageExp *loadSageExps(char *tableName, struct slName *nmList)
{
char *user = cfgOption("db.user");
char *password = cfgOption("db.password");
struct sqlConnection *sc = NULL;
char query[256];
struct sageExp *seList = NULL, *se=NULL;
char **row;
struct sqlResult *sr = NULL;
char *db = cgiUsualString("db", "hgFixed");
sc = sqlConnectRemote("localhost", user, password, db);
sqlSafef(query, sizeof query, "select * from sageExp order by num");
sr = sqlGetResult(sc,query);
while((row = sqlNextRow(sr)) != NULL)
{
se = sageExpLoad(row);
slAddHead(&seList,se);
}
sqlFreeResult(&sr);
sqlDisconnect(&sc);
slReverse(&seList);
return seList;
}
/** load the sage data by constructing a query based on the names in nmList
*/
struct sage *loadSageData(char *table, struct slName *nmList)
{
char *user = cfgOption("db.user");
char *password = cfgOption("db.password");
struct sqlConnection *sc = NULL;
struct dyString *query = newDyString(2048);
struct sage *sgList = NULL, *sg=NULL;
struct slName *nm =NULL;
char *db = cgiUsualString("db", "hgFixed");
char **row;
int count=0;
struct sqlResult *sr = NULL;
sc = sqlConnectRemote("localhost", user, password, db);
sqlDyStringPrintf(query, "select * from sage where ");
for(nm=nmList;nm!=NULL;nm=nm->next)
{
if (count++)
{
sqlDyStringPrintf(query," or uni=%s ", nm->name );
}
else
{
sqlDyStringPrintf(query," uni=%s ", nm->name);
}
}
sr = sqlGetResult(sc,query->string);
while((row = sqlNextRow(sr)) != NULL)
{
sg = sageLoad(row);
slAddHead(&sgList,sg);
}
sqlFreeResult(&sr);
sqlDisconnect(&sc);
slReverse(&sgList);
freeDyString(&query);
return sgList;
}
int main(int argc, char *argv[])
/* Process command line */
{
long enteredMainTime = clock1000();
cgiSpoof(&argc, argv);
termOpt = cgiOptionalString(CV_TERM);
tagOpt = cgiOptionalString(CV_TAG);
typeOpt = cgiOptionalString(CV_TYPE);
targetOpt = cgiOptionalString(CV_TARGET);
labelOpt = cgiOptionalString(CV_LABEL);
organismOpt = cgiUsualString(ORGANISM, organismOpt);
if (organismOpt != NULL)
{
organismOptLower=cloneString(organismOpt);
strLower(organismOptLower);
}
char *bgColor = cgiOptionalString("bgcolor");
if (bgColor)
htmlSetBgColor(strtol(bgColor, 0, 16));
htmlSetStyle(htmlStyleUndecoratedLink);
htmShell("ENCODE Controlled Vocabulary", doMiddle, "get");
cgiExitTime("hgEncodeVocab", enteredMainTime);
return 0;
}
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 webStartWrapperDetailedInternal(struct cart *theCart,
char *db, char *headerText, char *textOutBuf,
boolean withHttpHeader, boolean withLogo, boolean skipSectionHeader,
boolean withHtmlHeader)
/* output a CGI and HTML header with the given title in printf format */
{
char uiState[256];
char *scriptName = cgiScriptName();
boolean isEncode = FALSE;
if (theCart)
{
char *theGenome = NULL;
char *genomeEnc = NULL;
getDbAndGenome(theCart, &db, &theGenome, NULL);
genomeEnc = cgiEncode(theGenome);
safef(uiState, sizeof(uiState), "?%s=%s&%s=%s&%s=%u",
orgCgiName, genomeEnc,
dbCgiName, db,
cartSessionVarName(), cartSessionId(theCart));
}
else
{
uiState[0] = 0;
uiState[1] = 0;
}
if (db == NULL)
db = hDefaultDb();
boolean dbIsFound = hDbExists(db);
boolean haveBlat = FALSE;
if (dbIsFound)
haveBlat = hIsBlatIndexedDatabase(db);
if (scriptName == NULL)
scriptName = cloneString("");
/* don't output two headers */
if(webHeadAlreadyOutputed)
return;
if (sameString(cgiUsualString("action",""),"encodeReleaseLog") ||
rStringIn("EncodeDataVersions", scriptName))
isEncode = TRUE;
/* Preamble. */
dnaUtilOpen();
if (withHttpHeader)
puts("Content-type:text/html\n");
if (withHtmlHeader)
{
char *newString, *ptr1, *ptr2;
char *browserVersion;
if (btIE == cgiClientBrowser(&browserVersion, NULL, NULL) && *browserVersion < '8')
puts("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 3.2//EN\">");
else
puts("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Transitional//EN\" "
"\"http://www.w3.org/TR/html4/loose.dtd\">");
// Strict would be nice since it fixes atleast one IE problem (use of :hover CSS pseudoclass)
puts(
"<HTML>" "\n"
"<HEAD>" "\n"
);
printf("\t%s\n", headerText);
printf("\t<META HTTP-EQUIV=\"Content-Type\" CONTENT=\"text/html;CHARSET=iso-8859-1\">" "\n"
"\t<META http-equiv=\"Content-Script-Type\" content=\"text/javascript\">" "\n"
"\t<META HTTP-EQUIV=\"Pragma\" CONTENT=\"no-cache\">" "\n"
"\t<META HTTP-EQUIV=\"Expires\" CONTENT=\"-1\">" "\n"
"\t<TITLE>"
);
/* we need to take any HTML formatting out of the titlebar string */
newString = cloneString(textOutBuf);
for(ptr1=newString, ptr2=textOutBuf; *ptr2 ; ptr2++)
{
if (*ptr2 == '<')
{
for(; *ptr2 && (*ptr2 != '>'); ptr2++)
;
}
else
*ptr1++ = *ptr2;
}
*ptr1 = 0;
htmlTextOut(newString);
printf(" </TITLE>\n ");
webIncludeResourceFile("HGStyle.css");
if (extraStyle != NULL)
puts(extraStyle);
printf("</HEAD>\n");
printBodyTag(stdout);
htmlWarnBoxSetup(stdout);// Sets up a warning box which can be filled with errors as they occur
puts(commonCssStyles());
}
puts(
"<A NAME=\"TOP\"></A>" "\n"
"" "\n"
"<TABLE BORDER=0 CELLPADDING=0 CELLSPACING=0 WIDTH=\"100%\">" "\n");
if (withLogo)
{
puts("<TR><TH COLSPAN=1 ALIGN=\"left\">");
if (isEncode)
{
puts("<A HREF=\"http://www.genome.gov/10005107\" TARGET=\"_BLANK\">"
"<IMG SRC=\"../images/ENCODE_scaleup_logo.png\" height=50 ALT=\"ENCODE Project at NHGRI\">"
"</A>");
puts("<IMG SRC=\"../images/encodeDcc.jpg\" ALT=\"ENCODE Project at UCSC\">");
}
else
{
puts("<IMG SRC=\"../images/title.jpg\">");
}
puts("</TH></TR>" "\n"
"" "\n" );
}
/* Put up the hot links bar. */
char *menuStr = menuBar(theCart);
if(menuStr)
{
puts(menuStr);
}
if (endsWith(scriptName, "hgGateway") && geoMirrorEnabled())
{
// Show an opt-out alert if user is on a host to which user has been automatically redirected (just once, right after they have been redirected)
char *source = cgiOptionalString("source");
char *redirect = cgiOptionalString("redirect");
if (source != NULL && redirect != NULL && sameString(redirect, "auto"))
{
char *domain = cgiServerName();
char *port = cgiServerPort();
// We don't bother maintaining stuff in request URI, because it may contain items like hgsid and other host specific values
int newUriSize = 2048;
char *newUri = needMem(newUriSize);
safef(newUri, newUriSize, "http%s://%s:%s/cgi-bin/hgGateway?redirect=manual&source=%s",
cgiServerHttpsIsOn() ? "s" : "", source, port, domain);
printf("<TR><TD COLSPAN=3 id='redirectTd' onclick=\"javascript:document.getElementById('redirectTd').innerHTML='';\">"
"<div style=\"margin: 10px 25%%; border-style:solid; border-width:thin; border-color:#97D897;\">"
"<h3 style=\"background-color: #97D897; text-align: left; margin-top:0px; margin-bottom:0px;\">"
" You've been redirected to your nearest mirror - %s"
"<idiv style=\"float:right;\">[x]</idiv>"
"</h3> "
"<ul style=\"margin:5px;\">"
"<li>Take me back to <a href=\"%s\">%s</a>"
"<idiv style=\"float:right;\"><a href=\"../goldenPath/help/genomeEuro.html\">What is this?</a></idiv>"
"</li>"
"</ul>"
"</div>"
"</TD></TR>\n"
, domain, newUri, source );
}
}
if(!skipSectionHeader)
/* this HTML must be in calling code if skipSectionHeader is TRUE */
{
puts( // TODO: Replace nested tables with CSS (difficulty is that tables are closed elsewhere)
"<!-- +++++++++++++++++++++ CONTENT TABLES +++++++++++++++++++ -->" "\n"
"<TR><TD COLSPAN=3>\n"
"<div id=firstSection>"
" <!--outer table is for border purposes-->\n"
" <TABLE WIDTH='100%' BGCOLOR='#" HG_COL_BORDER "' BORDER='0' CELLSPACING='0' "
"CELLPADDING='1'><TR><TD>\n"
" <TABLE BGCOLOR='#" HG_COL_INSIDE "' WIDTH='100%' BORDER='0' CELLSPACING='0' "
"CELLPADDING='0'><TR><TD>\n"
" <div class='subheadingBar'><div class='windowSize' id='sectTtl'>"
);
htmlTextOut(textOutBuf);
puts(" </div></div>\n"
" <TABLE BGCOLOR='#" HG_COL_INSIDE "' WIDTH='100%' CELLPADDING=0>"
"<TR><TH HEIGHT=10></TH></TR>\n"
" <TR><TD WIDTH=10> </TD><TD>\n\n"
);
};
webPushErrHandlers();
/* set the flag */
webHeadAlreadyOutputed = TRUE;
} /* static void webStartWrapperDetailedInternal() */
void doExpRatio(struct trackDb *tdb, char *item, struct customTrack *ct)
/* Generic expression ratio deatils using microarrayGroups.ra file */
/* and not the expRecord tables. */
{
char *expScale = trackDbRequiredSetting(tdb, "expScale");
char *expStep = trackDbRequiredSetting(tdb, "expStep");
double maxScore = atof(expScale);
double stepSize = atof(expStep);
struct bed *bedList;
char *itemName = cgiUsualString("i2","none");
char *expName = (item == NULL) ? itemName : item;
char *tdbSetting = trackDbSettingOrDefault(tdb, "expColor", "redGreen");
char *colorVal = NULL;
enum expColorType colorScheme;
char colorVarName[256];
safef(colorVarName, sizeof(colorVarName), "%s.color", tdb->track);
colorVal = cartUsualString(cart, colorVarName, tdbSetting);
colorScheme = getExpColorType(colorVal);
if (sameWord(tdb->grp, "cancerGenomics"))
{
/* set global flag */
isCancerGenomicsTrack = TRUE;
}
if (!ct)
{
genericHeader(tdb, itemName);
bedList = loadMsBed(tdb, tdb->table, seqName, winStart, winEnd);
}
else if (ct->dbTrack)
{
genericHeader(tdb, itemName);
printCustomUrl(tdb, itemName, TRUE);
bedList = ctLoadMultScoresBedDb(ct, seqName, winStart, winEnd);
}
else
bedList = bedFilterListInRange(ct->bedList, NULL, seqName, winStart, winEnd);
if (bedList == NULL)
printf("<b>No Expression Data in this Range.</b>\n");
else if (expName && sameString(expName, "zoomInMore"))
printf("<b>Too much data to display in detail in this range.</b>\n");
else
{
struct microarrayGroups *groupings = NULL;
struct maGrouping *combineGroup;
struct hash *erHash = newHash(6);
int i;
if (!ct)
{
groupings = maGetTrackGroupings(database, tdb);
combineGroup = maCombineGroupingFromCart(groupings, cart, tdb->track);
}
else
combineGroup = maGetGroupingFromCt(ct);
maBedClumpGivenGrouping(bedList, combineGroup);
for (i = 0; i < combineGroup->numGroups; i++)
{
/* make stupid exprecord hash.perhaps eventually this won't be needed */
char id[16];
struct expRecord *er = basicExpRecord(combineGroup->names[i], i, 2);
safef(id, sizeof(id), "%d", i);
hashAdd(erHash, id, er);
}
puts("<h2></h2><p>\n");
msBedPrintTable(bedList, erHash, itemName, expName, -1*maxScore, maxScore,
stepSize, 2, msBedDefaultPrintHeader, msBedExpressionPrintRow,
printExprssnColorKey, getColorForExprBed, colorScheme);
hashTraverseEls(erHash, erHashElFree);
hashFree(&erHash);
microarrayGroupsFree(&groupings);
}
puts("<h2></h2><p>\n");
bedFreeList(&bedList);
}
void faNcbiToUcsc(char *inFile, char *out)
/* faNcbiToUcsc - Convert FA file from NCBI to UCSC format.. */
{
struct lineFile *lf = lineFileOpen(inFile, TRUE);
char outName[512];
char *line;
boolean split = cgiBoolean("split");
boolean ntLast = cgiBoolean("ntLast");
boolean encode = cgiBoolean("encode");
struct dnaSeq seq;
FILE *f = NULL;
char *wordBefore = cgiUsualString("wordBefore", "gb");
int wordIx = cgiUsualInt("wordIx", -1);
char *e = NULL;
char *nt = NULL;
ZeroVar(&seq);
if (split)
makeDir(out);
else
f = mustOpen(out, "w");
while (lineFileNext(lf, &line, NULL))
{
if (line[0] == '>')
{
if (ntLast || encode)
{
nt = NULL;
if (ntLast)
{
e = NULL;
nt = stringIn("NT_", line);
if (nt == NULL)
nt = stringIn("NG_", line);
if (nt == NULL)
nt = stringIn("NC_", line);
if (nt == NULL)
errAbort("Expecting NT_ NG_ or NC_in '%s'", line);
e = strchr(nt, '|');
if (e != NULL) *e = 0;
e = strchr(nt, ' ');
if (e != NULL) *e = 0;
}
else
{
nt = stringIn("|EN", line);
if (nt == NULL)
errAbort("Expecting EN in %s", line);
nt++;
nt = firstWordInLine(nt);
}
if (split)
{
sprintf(outName, "%s/%s.fa", out, nt);
carefulClose(&f);
f = mustOpen(outName, "w");
}
fprintf(f, ">%s\n", nt);
}
else
{
char *words[32];
int wordCount, i;
char *accession = NULL;
wordCount = chopString(line+1, "|", words, ArraySize(words));
if (wordIx >= 0)
{
if (wordIx >= wordCount)
errAbort("Sorry only %d words", wordCount);
accession = words[wordIx];
}
else
{
for (i=0; i<wordCount-1; ++i)
{
if (sameString(words[i], wordBefore))
{
accession = words[i+1];
break;
}
}
if (accession == NULL)
errAbort("Couldn't find '%s' line %d of %s",
wordBefore, lf->lineIx, lf->fileName);
}
chopSuffix(accession);
fprintf(f, ">%s\n", accession);
}
}
else
{
fprintf(f, "%s\n", line);
}
}
}
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");
}
static void webStartWrapperDetailedInternal(struct cart *theCart,
char *db, char *headerText, char *textOutBuf,
boolean withHttpHeader, boolean withLogo, boolean skipSectionHeader,
boolean withHtmlHeader)
/* output a CGI and HTML header with the given title in printf format */
{
char uiState[256];
char *scriptName = cgiScriptName();
boolean isEncode = FALSE;
if (theCart)
{
char *theGenome = NULL;
char *genomeEnc = NULL;
getDbAndGenome(theCart, &db, &theGenome, NULL);
genomeEnc = cgiEncode(theGenome);
safef(uiState, sizeof(uiState), "?%s=%s&%s=%s&%s=%s",
orgCgiName, genomeEnc,
dbCgiName, db,
cartSessionVarName(), cartSessionId(theCart));
}
else
{
uiState[0] = 0;
uiState[1] = 0;
}
if (db == NULL)
db = hDefaultDb();
boolean dbIsFound = hDbExists(db);
boolean haveBlat = FALSE;
if (dbIsFound)
haveBlat = hIsBlatIndexedDatabase(db);
if (scriptName == NULL)
scriptName = cloneString("");
/* don't output two headers */
if(webHeadAlreadyOutputed)
return;
if (sameString(cgiUsualString("action",""),"encodeReleaseLog") ||
rStringIn("EncodeDataVersions", scriptName))
isEncode = TRUE;
/* Preamble. */
dnaUtilOpen();
if (withHttpHeader)
puts("Content-type:text/html\n");
if (withHtmlHeader)
{
char *newString, *ptr1, *ptr2;
char *browserVersion;
if (btIE == cgiClientBrowser(&browserVersion, NULL, NULL) && *browserVersion < '8')
puts("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 3.2//EN\">");
else
puts("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Transitional//EN\" "
"\"http://www.w3.org/TR/html4/loose.dtd\">");
// Strict would be nice since it fixes atleast one IE problem (use of :hover CSS pseudoclass)
puts(
"<HTML>" "\n"
"<HEAD>" "\n"
);
printf("\t%s\n", headerText);
webPragmasEtc();
printf("\t<TITLE>");
/* we need to take any HTML formatting out of the titlebar string */
newString = cloneString(textOutBuf);
for(ptr1=newString, ptr2=textOutBuf; *ptr2 ; ptr2++)
{
if (*ptr2 == '<')
{
for(; *ptr2 && (*ptr2 != '>'); ptr2++)
;
}
else
*ptr1++ = *ptr2;
}
*ptr1 = 0;
htmlTextOut(newString);
printf(" </TITLE>\n ");
webIncludeResourceFile("HGStyle.css");
if (extraStyle != NULL)
puts(extraStyle);
printf("</HEAD>\n");
printBodyTag(stdout);
htmlWarnBoxSetup(stdout);// Sets up a warning box which can be filled with errors as they occur
puts(commonCssStyles());
}
webStartSectionTables();
if (withLogo)
{
puts("<TR><TH COLSPAN=1 ALIGN=\"left\">");
if (isEncode)
{
puts("<A HREF=\"http://www.genome.gov/10005107\" TARGET=\"_BLANK\">"
"<IMG SRC=\"../images/ENCODE_scaleup_logo.png\" height=50 ALT=\"ENCODE Project at NHGRI\">"
"</A>");
puts("<IMG SRC=\"../images/encodeDcc.jpg\" ALT=\"ENCODE Project at UCSC\">");
}
else
{
puts("<IMG SRC=\"../images/title.jpg\">");
}
puts("</TH></TR>" "\n"
"" "\n" );
}
/* Put up the hot links bar. */
char *menuStr = menuBar(theCart, db);
if(menuStr)
{
puts(menuStr);
}
if(!skipSectionHeader)
/* this HTML must be in calling code if skipSectionHeader is TRUE */
{
webFirstSection(textOutBuf);
};
webPushErrHandlers();
/* set the flag */
webHeadAlreadyOutputed = TRUE;
errAbortSetDoContentType(FALSE);
} /* static void webStartWrapperDetailedInternal() */
