void doMiddle()
/* doMiddle - put up middle part of web page, not including http and html headers/footers */
{
printf("<FORM ACTION=\"../cgi-bin/edwWebDeprecate\" METHOD=GET>\n");
struct sqlConnection *conn = edwConnectReadWrite(edwDatabase);
userEmail = edwGetEmailAndVerify();
if (userEmail == NULL)
logIn();
else if (cgiVarExists("fileList") && cgiVarExists("reason"))
tryToDeprecate(conn);
else
getFileListAndReason(conn);
printf("</FORM>");
}
int main(int argc, char *argv[])
/* Process command line. */
{
struct hash *liftHash = NULL;
cgiSpoof(&argc, argv);
if (argc != 6)
usage();
if (cgiVarExists("spacing"))
chromInsertsSetDefaultGapSize(cgiInt("spacing"));
if (cgiVarExists("lift"))
liftHash = readLift(cgiString("lift"));
ctgToChromFa(argv[1], argv[2], argv[3], argv[4], argv[5], liftHash);
return 0;
}
void doMiddle(struct cart *theCart)
/* Set up globals and make web page */
{
if (cgiVarExists("docId"))
{
if (cgiVarExists("meta"))
doDocIdMeta(theCart);
else if (cgiVarExists("report"))
doDocIdReport(theCart);
else if (cgiVarExists("lab"))
doLabContacts(theCart);
}
else
doStandard(theCart);
}
void outputSeq(DNA *dna, int dnaSize,
boolean hiliteRange, long startRange, long endRange,
FILE *out)
/* Write out sequence. */
{
struct dfm dfm;
int i;
char *seq = dna;
int size = dnaSize;
if (cgiBoolean("translate"))
{
int utr5 = 0;
int maxProtSize = (dnaSize+2)/3;
char *prot = needMem(maxProtSize + 1);
if (cgiVarExists("utr5"))
utr5 = cgiInt("utr5")-1;
startRange -= utr5;
endRange -= utr5;
startRange /= 3;
endRange /= 3;
dna += utr5;
seq = prot;
for (size = 0; size < maxProtSize; ++size)
{
if ((*prot++ = lookupCodon(dna)) == 0)
break;
dna += 3;
}
*prot = 0;
}
initDfm(&dfm, 10, 50, TRUE, hiliteRange, startRange, endRange, out);
for (i=0; i<size; ++i)
dfmOut(&dfm, seq[i]);
}
void doMiddle(struct cart *theCart)
/* Set up globals and make web page */
{
char *database = cgiOptionalString("db");
char *rtdbServer = cfgOption("rtdb.server");
char *rtdbPort = cfgOption("rtdb.port");
char *rtdbChoices = cfgOption("rtdb.databases");
struct slName *dbs = slNameListFromComma(rtdbChoices);
cart = theCart;
cartWebStart(cart, database, "MGC RTDB Update");
if (!rtdbServer)
errAbort("rtdb.update not defined in the hg.conf file. "
"Chances are this CGI isn't meant for this machine.");
if (!rtdbPort)
errAbort("rtdb.update not defined in the hg.conf file. "
"Chances are this CGI isn't meant for this machine.");
/* create HMTL form if button wasn't pressed. Otherwise, run the update */
if (!cgiVarExists("RTDBSubmit"))
makeForm(dbs);
else if ((database == NULL) || (!slNameInList(dbs, database)))
{
makeForm(dbs);
printf("<br>Error: Select one of databases listed.");
}
else
updateServer(rtdbServer, rtdbPort, database);
cartWebEnd();
slNameFreeList(&dbs);
}
void checkYbr(char *agpFile, char *faFile, char *mdFile)
/* checkYbr - Check NCBI assembly (aka Yellow Brick Road). */
{
struct hash *hash = newHash(0);
struct contig *contigList = NULL, *contig;
int problemCount = 0;
contigList = contigsFromAgp(agpFile, hash);
printf("Read %d contigs from %s\n", slCount(contigList), agpFile);
if (cgiVarExists("checkUs"))
{
printf("Checking our fa files for size\n");
checkOurDir(cgiString("checkUs"), contigList, hash);
}
else
{
problemCount += flagMd(mdFile, hash);
printf("Verifying sequence sizes in %s\n", faFile);
problemCount += flagFa(faFile, hash);
for (contig = contigList; contig != NULL; contig = contig->next)
{
if (contig->gotFa && contig->gotMd)
continue;
++problemCount;
if (!contig->gotFa)
printf("No %s in %s\n", contig->name, faFile);
if (!contig->gotMd)
printf("No %s in %s\n", contig->name, mdFile);
}
printf("%d problems detected\n", problemCount);
}
}
int main(int argc, char *argv[])
{
cgiSpoof(&argc, argv);
if (cgiVarExists("pbt.reset"))
resetVars();
/* call cartHtmlShellPbGlobal to accomodate situations that PB not entered from GB */
cartHtmlShellPbGlobal("UCSC Proteome Browser V1.1", doMiddle, hUserCookie(), excludeVars, NULL);
return 0;
}
boolean okToDeprecateThisFile(struct sqlConnection *conn, int fId, char *userEmail)
/* Return true if it is OK to deprecate this file */
{
if (checkOwnership(conn, fId, userEmail))
return TRUE;
else if (cgiVarExists("allowBox"))
return TRUE;
else
return FALSE;
}
void doMiddle()
/* doMiddle - put up middle part of web page, not including http and html headers/footers */
{
pushWarnHandler(localWarn);
printf("<FORM ACTION=\"../cgi-bin/edwWebSubmit\" METHOD=GET>\n");
struct sqlConnection *conn = edwConnectReadWrite(edwDatabase);
userEmail = edwGetEmailAndVerify();
if (userEmail == NULL)
logIn();
else if (cgiVarExists(stopButtonName))
stopUpload(conn);
else if (cgiVarExists("submitUrl"))
submitUrl(conn);
else if (cgiVarExists("monitor"))
monitorSubmission(conn);
else
getUrl(conn);
printf("</FORM>");
}
void doMiddle()
/* Write middle part of .html. */
{
DNA *targetDna;
char *chrom;
int tStart, tEnd;
struct xaAli *xa;
int bothStart, bothEnd;
char cbCosmidName[256];
char *s;
/* Get input variables from CGI. */
char *qOrganism = cgiString("qOrganism");
char *tOrganism = cgiString("tOrganism");
char *query = cgiString("query");
char *target = cgiString("target");
char *strandString = cgiString("strand");
char strand = strandString[0];
boolean showSym = cgiBoolean("symbols");
boolean gotClickPos = cgiVarExists("clickPos");
double clickPos;
if (gotClickPos) clickPos = cgiDouble("clickPos");
strcpy(cbCosmidName, query);
if ((s = strrchr(cbCosmidName, '.')) != NULL)
*s = 0;
/* Get xaAli. */
xa = getOneXaAli(qOrganism, query);
printf("<H2>Alignment of <I>C. briggsae</I> %s:%d-%d and <I>C. elegans</I> %s</H2>\n",
cbCosmidName, xa->qStart, xa->qEnd, target);
htmlParagraph("<I>C. briggsae</I> appears on top. Coding regions in <I>C. elegans</I> are in upper case.");
/* Get display window. */
if (!wormParseChromRange(target, &chrom, &tStart, &tEnd))
errAbort("Target %s isn't formatted correctly", target);
/* Figure out intersection of display window and xeno-alignment */
bothStart = max(xa->tStart, tStart);
bothEnd = min(xa->tEnd, tEnd);
/* Get upper-cased-exon target DNA. */
targetDna = wormChromPartExonsUpper(chrom, bothStart, bothEnd - bothStart);
upcCorresponding(targetDna, bothEnd - bothStart, xa->tSym, bothStart - xa->tStart);
printf("<TT><PRE>");
showTargetRange(xa, bothStart - xa->tStart, bothEnd-bothStart, strand, showSym);
printf("</TT></PRE>");
}
int main(int argc, char *argv[])
/* Process command line. */
{
cgiSpoof(&argc, argv);
if (cgiVarExists("db"))
{
database=cgiOptionalString("db");
}
cartEmptyShell(doMiddle, hUserCookie(), excludeVars, oldVars);
return 0;
}
void dispatchPage()
/* Look at command variables in cart and figure out which
* page to draw. */
{
struct sqlConnection *conn = hAllocConn(database);
if (checkAndClear(hggConfigure))
{
configurePage();
}
else if (checkAndClear(hggConfigureOne))
{
configureOnePage();
}
else if (checkAndClear(hggUpload))
{
uploadPage();
}
else if (checkAndClear(hggSubmitUpload))
{
submitUpload(conn);
}
else if (checkAndClear(hggImport))
{
importPage(conn);
}
else if (checkAndClear(hggSubmitImport))
{
submitImport();
}
else if (checkAndClear(hggCorrelate))
{
correlatePage(conn);
}
else if (checkAndClear(hggBrowse))
{
browseRegions(conn);
}
else if (checkAndClear(hggSort))
{
sortGenes(conn);
}
else
{
/* Default case - start fancy web page. */
if (cgiVarExists(hggPsOutput))
handlePostscript(conn);
else
mainPage(conn);
}
cartRemovePrefix(cart, hggDo);
}
int main(int argc, char *argv[])
/* Process command line. */
{
cgiSpoof(&argc, argv);
userCount = cgiOptionalInt("userCount", userCount);
randSeed = cgiOptionalInt("randSeed", (int)getpid());
verboseSetLevel(cgiOptionalInt("verbose", 1));
readOnly = cgiVarExists("readOnly");
srand(randSeed);
if (argc != 7)
usage();
cartSimNoInsert(argv[1], argv[2], argv[3], argv[4], argv[5], argv[6]);
return 0;
}
int main(int argc, char *argv[])
{
long enteredMainTime = clock1000();
measureTime(NULL);
setUdcCacheDir();
browserName = hBrowserName();
organization = "UCSC";
/* Push very early error handling - this is just
* for the benefit of the cgiVarExists, which
* somehow can't be moved effectively into doMiddle. */
htmlPushEarlyHandlers();
cgiSpoof(&argc, argv);
char * link = webTimeStampedLinkToResourceOnFirstCall("HGStyle.css",TRUE); // resource file link
if (link) // wrapped in html
htmlSetStyle(link);
oldVars = hashNew(10);
if (cgiVarExists("hgt.redirectTool"))
{
printf("Content-type: text/html\n\n");
cart = cartForSession(hUserCookie(), NULL, NULL);
printf("<html><body>\n");
printf("<form id=\"redirForm\" method=\"POST\" action=\"http://tefor.net/crisporMax/crispor.cgi\">\n");
printf("<input type=\"hidden\" name=\"pos\" value=\"%s\">", cartString(cart, "position"));
printf("<input type=\"hidden\" name=\"org\" value=\"%s\">", cartString(cart, "db"));
printf("<input type=\"hidden\" name=\"pam\" value=\"NGG\">\n");
// a hidden submit button, see
// http://stackoverflow.com/questions/477691/submitting-a-form-by-pressing-enter-without-a-submit-button
printf("<input type=\"submit\" style=\"position: absolute; left: -9999px; width: 1px; height: 1px;\">\n");
printf("</form>\n");
// a little javascript that clicks the submit button
printf("<script>document.getElementById(\"redirForm\").submit();</script>\n");
printf("</body></html>\n");
}
else
cartHtmlShell("UCSC Genome Browser v"CGI_VERSION, doMiddle, hUserCookie(), excludeVars, oldVars);
if (measureTiming)
measureTime("Time to write and close cart");
if (measureTiming)
{
fprintf(stdout, "<span class='timing'>Overall total time: %ld millis<br /></span>\n",
clock1000() - enteredMainTime);
}
cgiExitTime("hgTracks", enteredMainTime);
return 0;
}
void doMiddle()
{
char *preIntron, *startIntron, *endIntron, *postIntron;
int count = 0;
int matchCount = 0;
int maxCount;
struct nameOff *matchList;
boolean invert = cgiVarExists("Invert");
preIntron = cgiString("preIntron");
startIntron = cgiString("startIntron");
endIntron = cgiString("endIntron");
postIntron = cgiString("postIntron");
/* Just for debugging cut search short if matches special magic */
maxCount = atoi(preIntron);
if (maxCount <= 0)
maxCount = 0x7ffffff;
eraseWhiteSpace(preIntron);
eraseWhiteSpace(startIntron);
eraseWhiteSpace(endIntron);
eraseWhiteSpace(postIntron);
tolowers(preIntron);
tolowers(startIntron);
tolowers(endIntron);
tolowers(postIntron);
matchList = scanIntronFile(preIntron, startIntron, endIntron, postIntron, invert);
if (matchList == NULL)
errAbort("Sorry, no matches to %s%s %s %s %s", (invert ? "inverted " : ""), preIntron, startIntron, endIntron, postIntron);
printf("<P>%d introns matching %s%s(%s %s)%s. ", slCount(matchList),
(invert ? "inverted " : ""), preIntron, startIntron, endIntron, postIntron);
printf("Shortcut to <A HREF=\"#1\">frequency counts.</A></P>");
htmlHorizontalLine();
showMatches(matchList);
htmlHorizontalLine();
printf("<TT><PRE>");
printf("<A NAME=\"1\"></A>");
printAllHistograms();
printf("</TT></PRE>");
}
void autoXml(char *dtdxFile, char *outRoot)
/* autoXml - Generate structures code and parser for XML file from DTD-like spec. */
{
struct dtdElement *elList = NULL;
struct hash *elHash = NULL;
char hName[512], cName[512];
char outDir[256];
splitPath(outRoot, outDir, prefix, NULL);
if (cgiVarExists("prefix"))
strcpy(prefix, cgiString("prefix"));
if (outDir[0] != 0)
makeDir(outDir);
dtdParse(dtdxFile, prefix, textField, &elList, &elHash);
printf("Parsed %d elements in %s\n", slCount(elList), dtdxFile);
sprintf(hName, "%s.h", outRoot);
makeH(elList, hName);
sprintf(cName, "%s.c", outRoot);
makeC(elList, cName, hName);
printf("Generated code in %s\n", cName);
}
int main(int argc, char *argv[])
/* Process command line. */
{
long enteredMainTime = clock1000();
uglyTime(NULL);
cgiSpoof(&argc, argv);
setUdcCacheDir();
oldCart = hashNew(0);
if (cgiVarExists(hgpDoDownload)) /* use cgiVars -- do not commit to any cart method yet */
{
struct sqlConnection *conn = sqlConnect(visiDb);
cart = cartAndCookieNoContent(hUserCookie(), excludeVars, oldCart);
doDownload(conn);
cartCheckout(&cart);
}
else
{
cartEmptyShell(doMiddle, hUserCookie(), excludeVars, oldCart);
}
cgiExitTime("hgVisiGene", enteredMainTime);
return 0;
}
int main(int argc, char *argv[])
{
long enteredMainTime = clock1000();
measureTime(NULL);
browserName = hBrowserName();
organization = "UCSC";
/* Push very early error handling - this is just
* for the benefit of the cgiVarExists, which
* somehow can't be moved effectively into doMiddle. */
htmlPushEarlyHandlers();
cgiSpoof(&argc, argv);
char * link = webTimeStampedLinkToResourceOnFirstCall("HGStyle.css",TRUE); // resource file link
if (link) // wrapped in html
htmlSetStyle(link);
oldVars = hashNew(10);
if (cgiVarExists("hgt.redirectTool"))
{
printf("Content-type: text/html\n\n");
errAbortSetDoContentType(FALSE);
cart = cartForSession(hUserCookie(), NULL, NULL);
extToolRedirect(cart, cgiString("hgt.redirectTool"));
}
else
cartHtmlShell("UCSC Genome Browser v"CGI_VERSION, doMiddle, hUserCookie(), excludeVars, oldVars);
if (measureTiming)
measureTime("Time to write and close cart");
if (measureTiming)
{
fprintf(stdout, "<span class='timing'>Overall total time: %ld millis<br /></span>\n",
clock1000() - enteredMainTime);
}
cgiExitTime("hgTracks", enteredMainTime);
return 0;
}
void doMiddle()
/* Write HTML file to stdout. */
{
char *mapName;
if ((mapName = cgiOptionalString("map")) != NULL)
{
printf("<TT>\n");
doMap(mapName);
}
else if (cgiVarExists("contig"))
{
doFuzzyFind();
}
else
{
char *bacAcc = cgiString("bacAcc");
char *repeatMask = cgiString("repeatMask");
int trim = cgiInt("trim");
if (trim < 0)
trim = 0;
bacTrack(bacAcc, trim, repeatMask);
}
}
void doMiddle(struct cart *theCart)
/* Print the body of an html file. */
{
char cond_str[255];
struct sqlConnection *conn;
char *proteinAC;
char *chp, *chp1, *chp9;
char *debugTmp = NULL;
char *chromStr, *cdsStartStr, *cdsEndStr, posStr[255];
char *supportedGenomeDatabase;
char *answer;
char *queryID;
/* Initialize layout and database. */
cart = theCart;
/* Uncomment this to see parameters for debugging. */
/* Be careful though, it breaks if custom track
* is more than 4k */
/*
{ struct dyString *state = cgiUrlString();
hPrintf("State: %s\n", state->string);
}
*/
queryID = cartOptionalString(cart, "proteinID");
if (sameString(queryID, ""))
{
hUserAbort("Please go back and enter a gene symbol or a Swiss-Prot/TrEMBL protein ID.\n");
}
if (cgiVarExists("db"))
{
/* if db is known, get key variables set */
proteinInSupportedGenome = TRUE;
database = cgiOptionalString("db");
organism = hDbOrganism(database);
protDbName = hPdbFromGdb(database);
proteinID = strdup(queryID);
}
else
{
protCntInSwissByGene = searchProteinsInSwissProtByGene(queryID);
/* no CGI 'db' variable means it did not come in from GB but from pbGateway */
/* search existing GB databases to see if this protein can be found */
protCntInSupportedGenomeDb =
searchProteinsInSupportedGenomes(queryID, &supportedGenomeDatabase);
if ((protCntInSupportedGenomeDb > 1) || protCntInSwissByGene >= 1)
{
/* more than 1 proteins match the query ID, present selection web page */
proteinInSupportedGenome = 1;
presentProteinSelections(queryID, protCntInSwissByGene, protCntInSupportedGenomeDb);
return;
}
else
{
if (protCntInSupportedGenomeDb == 1)
{
/* one and only one protein found in a genome DB that support KG and PB */
proteinInSupportedGenome = TRUE;
database = strdup(supportedGenomeDatabase);
organism = hDbOrganism(database);
protDbName = hPdbFromGdb(database);
proteinID=strdup(queryID);
}
else
{
/* not found in genome DBs that support KG/PB */
/* now search PROTEOME_DB_NAMES to see if this protein is there. */
answer = uniProtFindPrimAcc(queryID);
if (answer == NULL)
{
hUserAbort("'%s' does not seem to be a valid UniProtKB protein ID or a gene "
"symbol.<br><br>Click <A HREF=\"../cgi-bin/pbGateway\">here</A> "
"to start another query.", queryID);
}
proteinInSupportedGenome = FALSE;
database = strdup(GLOBAL_PB_DB);
organism = strdup("");
protDbName = strdup(PROTEOME_DB_NAME);
proteinID = strdup(answer);
}
}
if (proteinInSupportedGenome)
{
spConn = sqlConnect(database);
sqlSafefFrag(cond_str, sizeof(cond_str), "alias='%s'", queryID);
proteinID = sqlGetField(database, "kgSpAlias", "spID", cond_str);
sqlSafefFrag(cond_str, sizeof(cond_str), "spID='%s'", proteinID);
answer = sqlGetField(database, "kgXref", "spDisplayID", cond_str);
sqlSafefFrag(cond_str, sizeof(cond_str), "proteinID='%s'", answer);
chromStr = sqlGetField(database, "knownGene", "chrom", cond_str);
if (chromStr)
{
cdsStartStr = sqlGetField(database, "knownGene", "cdsStart", cond_str);
cdsEndStr = sqlGetField( database, "knownGene", "cdsEnd", cond_str);
safef(posStr, sizeof(posStr), "%s:%s-%s", chromStr, cdsStartStr, cdsEndStr);
positionStr = strdup(posStr);
cartSetString(cart, "position", positionStr);
cartSetString(cart, "organism", organism);
}
}
}
/* print out key variables for debugging */
/* printf("<br>before enter main section: <br>proteinInSupportedGenome=%d<br>proteinID=%s <br>database=%s <br>organism=%s <br>protDbName=%s\n",
proteinInSupportedGenome, proteinID, database, organism, protDbName);fflush(stdout);
*/
if (hTableExists(database, "kgProtMap2"))
{
kgVersion = KG_III;
strcpy(kgProtMapTableName, "kgProtMap2");
}
debugTmp = cartUsualString(cart, "hgDebug", "off");
if(sameString(debugTmp, "on"))
hgDebug = TRUE;
else
hgDebug = FALSE;
conn = hAllocConn(database);
hgsid = cartOptionalString(cart, "hgsid");
if (hgsid != NULL)
{
safef(hgsidStr, sizeof(hgsidStr), "&hgsid=%s", hgsid);
}
else
{
strcpy(hgsidStr, "");
}
/* check proteinID to see if it is a valid SWISS-PROT/TrEMBL accession or display ID */
/* then assign the accession number to global variable proteinID */
sqlSafefFrag(cond_str, sizeof(cond_str), "accession='%s'", proteinID);
proteinAC = sqlGetField(protDbName, "spXref3", "accession", cond_str);
if (proteinAC == NULL)
{
sqlSafefFrag(cond_str, sizeof(cond_str), "displayID='%s'", proteinID);
proteinAC = sqlGetField(protDbName, "spXref3", "accession", cond_str);
if (proteinAC == NULL)
{
hUserAbort("'%s' does not seem to be a valid Swiss-Prot/TrEMBL protein ID or gene symbol.<br><br>Click <A HREF=\"../cgi-bin/pbGateway\">here</A> to start another query."
, proteinID);
}
else
{
protDisplayID = proteinID;
proteinID = proteinAC;
}
}
else
{
sqlSafefFrag(cond_str, sizeof(cond_str), "accession='%s'", proteinID);
protDisplayID = sqlGetField(protDbName, "spXref3", "displayID", cond_str);
}
if (proteinInSupportedGenome)
{
if (kgVersion == KG_III)
{
sqlSafefFrag(cond_str, sizeof(cond_str), "spId='%s'", proteinID);
mrnaID = sqlGetField(database, "kgXref", "kgId", cond_str);
}
else
{
sqlSafefFrag(cond_str, sizeof(cond_str), "proteinID='%s'", protDisplayID);
mrnaID = sqlGetField(database, "knownGene", "name", cond_str);
}
}
else
{
mrnaID = NULL;
positionStr = NULL;
}
sqlSafefFrag(cond_str, sizeof(cond_str), "accession='%s'", proteinID);
description = sqlGetField(protDbName, "spXref3", "description", cond_str);
if (positionStr != NULL)
{
chp = strstr(positionStr, ":");
*chp = '\0';
prevGBChrom = cloneString(positionStr);
chp1 = chp + 1;
chp9 = strstr(chp1, "-");
*chp9 = '\0';
prevGBStartPos = atoi(chp1);
chp1 = chp9 + 1;
prevGBEndPos = atoi(chp1);
}
else
{
prevGBChrom = NULL;
prevGBStartPos = -1;
prevGBEndPos = -1;
}
/* Do main display. */
if (cgiVarExists("pbt.psOutput"))
handlePostscript();
else
{
doTrackForm(NULL, NULL);
}
}
void doMiddle()
{
char *seqName;
boolean intronsLowerCase = TRUE;
boolean intronsParenthesized = FALSE;
boolean hiliteNear = FALSE;
int startRange = 0;
int endRange = 0;
boolean gotRange = FALSE;
struct dnaSeq *cdnaSeq;
boolean isChromRange = FALSE;
DNA *dna;
char *translation = NULL;
seqName = cgiString("geneName");
seqName = trimSpaces(seqName);
if (cgiVarExists("intronsLowerCase"))
intronsLowerCase = cgiBoolean("intronsLowerCase");
if (cgiVarExists("intronsParenthesized"))
intronsParenthesized = cgiBoolean("intronsParenthesized");
if (cgiVarExists("startRange") && cgiVarExists("endRange" ))
{
startRange = cgiInt("startRange");
endRange = cgiInt("endRange");
gotRange = TRUE;
}
if (cgiVarExists("hiliteNear"))
{
hiliteNear = TRUE;
}
fprintf(stdout, "<P><TT>\n");
/* The logic here is a little complex to optimize speed.
* If we can decide what type of thing the name refers to by
* simply looking at the name we do. Otherwise we have to
* search the database in various ways until we get a hit. */
if (wormIsNamelessCluster(seqName))
{
isChromRange = TRUE;
}
else if (wormIsChromRange(seqName))
{
isChromRange = TRUE;
}
else if (getWormGeneDna(seqName, &dna, TRUE))
{
if (cgiBoolean("litLink"))
{
char nameBuf[64];
char *geneName = NULL;
char *productName = NULL;
char *coding;
int transSize;
struct wormCdnaInfo info;
printf("<H3>Information and Links for %s</H3>\n", seqName);
if (wormInfoForGene(seqName, &info))
{
if (info.description)
printf("<P>%s</P>\n", info.description);
geneName = info.gene;
productName = info.product;
}
else
{
if (wormIsGeneName(seqName))
geneName = seqName;
else if (wormGeneForOrf(seqName, nameBuf, sizeof(nameBuf)))
geneName = nameBuf;
}
coding = cloneUpperOnly(dna);
transSize = 1 + (strlen(coding)+2)/3;
translation = needMem(1+strlen(coding)/3);
dnaTranslateSome(coding, translation, transSize);
freez(&coding);
if (geneName)
{
printf("<A HREF=\"http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=4&db=m"
"&term=C+elegans+%s&dispmax=50&relentrezdate=No+Limit\">", geneName);
printf("PubMed search on gene: </A>%s<BR>\n", geneName);
}
if (productName)
{
char *encoded = cgiEncode(productName);
printf("<A HREF=\"http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=4&db=m"
"&term=%s&dispmax=50&relentrezdate=No+Limit\">", encoded);
printf("PubMed search on product:</A> %s<BR>\n", productName);
freeMem(encoded);
}
/* Process name to get rid of isoform letter for Proteome. */
if (geneName)
strcpy(nameBuf, geneName);
else
{
strcpy(nameBuf, seqName);
#ifdef NEVER
/* Sometimes Proteome requires the letter after the orf name
* in alt-spliced cases, sometimes it can't handle it.... */
nameLen = strlen(nameBuf);
if (wormIsOrfName(nameBuf) && isalpha(nameBuf[nameLen-1]))
{
char *dotPos = strrchr(nameBuf, '.');
if (dotPos != NULL && isdigit(dotPos[1]))
nameBuf[nameLen-1] = 0;
}
#endif /* NEVER */
}
printf("<A HREF=\"http://www.wormbase.org/db/seq/sequence?name=%s;class=Sequence\">", seqName);
printf("WormBase link on:</A> %s<BR>\n", seqName);
printf("<A HREF=\"http://www.proteome.com/databases/WormPD/reports/%s.html\">", nameBuf);
printf("Proteome link on:</A> %s<BR>\n<BR>\n", nameBuf);
printf("<A HREF=#DNA>Genomic DNA Sequence</A><BR>\n");
if (hiliteNear)
printf("<A HREF=\"#CLICKED\">Shortcut to where you clicked in gene</A><BR>");
printf("<A HREF=#protein>Translated Protein Sequence</A><BR>\n");
htmlHorizontalLine();
printf("<A NAME=DNA></A>");
printf("<H3>%s Genomic DNA sequence</H3>", seqName);
}
if (!intronsLowerCase)
tolowers(dna);
if (hiliteNear)
{
if (!gotRange)
{
double nearPos = cgiDouble("hiliteNear");
int rad = 5;
int dnaSize = strlen(dna);
long mid = (int)(dnaSize * nearPos);
startRange = mid - rad;
if (startRange < 0) startRange = 0;
endRange = mid + rad;
if (endRange >= dnaSize) endRange = dnaSize - 1;
}
}
outputSeq(dna, strlen(dna), hiliteNear, startRange, endRange, stdout);
freez(&dna);
}
else if (wormCdnaSeq(seqName, &cdnaSeq, NULL))
{
outputSeq(cdnaSeq->dna, cdnaSeq->size, FALSE, 0, 0, stdout);
}
else
{
isChromRange = TRUE;
}
if (isChromRange)
{
char *chromId;
int start, end;
char strand = '+';
int size;
if (!wormGeneRange(seqName, &chromId, &strand, &start, &end))
errAbort("Can't find %s",seqName);
size = end - start;
if (intronsLowerCase)
dna = wormChromPartExonsUpper(chromId, start, size);
else
{
dna = wormChromPart(chromId, start, size);
touppers(dna);
}
if (cgiVarExists("strand"))
strand = cgiString("strand")[0];
if (strand == '-')
reverseComplement(dna, size);
outputSeq(dna, size, FALSE, 0, 0, stdout);
}
if (translation != NULL)
{
htmlHorizontalLine();
printf("<A NAME=protein></A>");
printf("<H3>Translated Protein of %s</H3>\n", seqName);
outputSeq(translation, strlen(translation), FALSE, 0, 0, stdout);
freez(&translation);
}
fprintf(stdout, "</TT></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 ctgToChromFa(char *chromName, char *insertFile, char *chromDir,
char *orderLst, char *outName, struct hash *liftHash)
/* ctgToChromFa - convert contig level fa files to chromosome level. */
{
struct hash *uniq = newHash(0);
struct bigInsert *bi;
struct chromInserts *chromInserts;
struct hash *insertHash = newHash(9);
struct lineFile *lf = lineFileOpen(orderLst, TRUE);
FILE *f = mustOpen(outName, "w");
char ctgFaName[512];
char *words[2];
int liftChromSize = 0;
int actualChromSize = 0;
boolean isFirst = TRUE;
chromInsertsRead(insertFile, insertHash);
chromInserts = hashFindVal(insertHash, chromName);
fprintf(f, ">%s\n", chromName);
while (lineFileNextRow(lf, words, 1))
{
char *contig = words[0];
int nSize;
if (liftHash != NULL)
{
struct lift *lift = hashMustFindVal(liftHash, contig);
nSize = lift->nBefore;
liftChromSize = lift->chromSize;
}
else
nSize = chromInsertsGapSize(chromInserts, rmChromPrefix(contig), isFirst);
hashAddUnique(uniq, contig, NULL);
addN(f, nSize);
actualChromSize += nSize;
isFirst = FALSE;
sprintf(ctgFaName, "%s/%s/%s.fa", chromDir, contig, contig);
if (fileExists(ctgFaName))
{
actualChromSize += addFa(f, ctgFaName);
}
else
{
warn("%s does not exist\n", ctgFaName);
if (!cgiVarExists("missOk"))
noWarnAbort();
}
}
lineFileClose(&lf);
if (chromInserts != NULL)
if ((bi = chromInserts->terminal) != NULL)
{
addN(f, bi->size);
actualChromSize += bi->size;
}
if (liftHash != NULL)
{
if (actualChromSize > liftChromSize)
errAbort("Error: chromosome size from lift file is %d, but actual fa size is %d. Possible inconsistency between lift and inserts?",
liftChromSize, actualChromSize);
else if (actualChromSize < liftChromSize)
addN(f, (liftChromSize - actualChromSize));
}
if (linePos != 0)
fputc('\n', f);
fclose(f);
}
void doMiddle()
/* Write what goes between BODY and /BODY */
{
pushWarnHandler(localWarn);
if (!cgiServerHttpsIsOn())
usage();
struct sqlConnection *conn = edwConnectReadWrite();
printf("<FORM ACTION=\"edwWebRegisterScript\" METHOD=POST>\n");
printf("<B>Register Script with ENCODE Data Warehouse</B><BR>\n");
#ifdef SOON
uglyf("HTTP_AUTHENTICATION: '%s'<BR>\n", getenv("HTTP_AUTHENTICATION"));
uglyf("HTTP_AUTHORIZATION: '%s'<BR>\n", getenv("HTTP_AUTHORIZATION"));
dumpEnv(mainEnv);
#endif
if (userEmail == NULL)
{
printf("Please sign in:");
printf("<INPUT TYPE=BUTTON NAME=\"signIn\" VALUE=\"sign in\" id=\"signin\">");
}
else if (cgiVarExists("description"))
{
struct edwUser *user = edwUserFromEmail(conn, userEmail);
if (user == NULL)
edwWarnUnregisteredUser(userEmail);
else
{
char password[HEXED_32_SIZE];
edwRandomHexed32(password);
char babyName[HEXED_32_SIZE];
edwRandomBabble(babyName, sizeof(babyName));
edwRegisterScript(conn, user, babyName, password, cgiString("description"));
printf("Script now registered.<BR>\n");
printf("The script user name is %s.<BR>\n", babyName);
printf("The script password is %s.<BR>\n", password);
printf("Please save the script user name and password somewhere. ");
puts("Please pass these two and the URL");
puts(" of your validated manifest file (validated.txt) to our server to submit data.");
puts("Construct a URL of the form:<BR>");
printf("<PRE>https://encodedcc.sdsc.edu/cgi-bin/edwScriptSubmit"
"?user=%s&password=%s&url=%s\n</PRE>",
babyName, password,
cgiEncode("http://your.host.edu/your_dir/validated.txt"));
puts("That is pass the CGI encoded variables user, password, and url to the ");
puts("web services CGI at");
puts("https://encodedcc.sdsc.edu/cgi-bin/edwScriptSubmit. ");
puts("You can use the http://encodedcc.sdsc.edu/cgi-bin/edwWebBrowse site to ");
puts("monitor your submission interactively. Please contact your wrangler if you ");
puts("have any questions.<BR>");
cgiMakeButton("submit", "Register another script");
}
printf(" ");
edwPrintLogOutButton();
}
else
{
struct edwUser *user = edwUserFromEmail(conn, userEmail);
edwPrintLogOutButton();
if (user == NULL)
edwWarnUnregisteredUser(userEmail);
else
{
printf("%s is authorized to register a new script<BR>\n", userEmail);
printf("<BR>Script description:\n");
cgiMakeTextVar("description", NULL, 80);
cgiMakeSubmitButton();
}
}
printf("</FORM>\n");
}
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");
}
int main(int argc, char *argv[])
/* Process command line. */
{
pushCarefulMemHandler(100000000);
cgiSpoof(&argc, argv);
htmlSetStyle(htmlStyleUndecoratedLink);
htmlSetBgColor(HG_CL_OUTSIDE);
oldCart = hashNew(10);
cart = cartAndCookie(hUserCookie(), excludeVars, oldCart);
getDbAndGenome(cart, &database, &genome, oldCart);
//hSetDb(database);
conn = hAllocConn(database);
database = strdup("h1n1");
/* Get sortOn. Revert to default by subject Id. */
orderOn = cartUsualString(cart, orderVarName, "+subjId");
displayCountString = cartUsualString(cart, countVarName, "50");
if (sameString(displayCountString, "all"))
displayCount = BIGNUM;
else
displayCount = atoi(displayCountString);
colList = getColumns(conn);
if (cgiVarExists("submit_filter"))
{
struct dyString *head = dyStringNew(1024);
boolean redir = cgiVarExists(redirectName);
struct subjInfo *subjList = NULL;
struct column *ordList = colList;
struct column *ord = curOrder(ordList);
subjList = getOrderedList(ord, colList, conn, BIGNUM);
saveSubjList(subjList);
if ((!subjList || redir))
{
if (subjList && redir)
{
dyStringPrintf(head,
"<META HTTP-EQUIV=\"REFRESH\" CONTENT=\"0;URL=/cgi-bin/%s\">"
"<META HTTP-EQUIV=\"Pragma\" CONTENT=\"no-cache\">"
"<META HTTP-EQUIV=\"Expires\" CONTENT=\"-1\">"
, cgiString(redirectName));
cartRemove(cart, redirectName);
}
htmStartWithHead(stdout, head->string, "GISAID Table View");
if (!subjList) /* if everything has been filtered out, we'll have to go back */
{
hPrintf("No subject(s) found with the filtering conditions specified.<br>");
hPrintf("Click <a href=\"gisaidTable?gisaidTable.do.advFilter=filter+%%28now+on%%29\">here</a> "
"to return to Select Subjects.<br>");
}
cartCheckout(&cart);
htmlEnd();
hFreeConn(&conn);
return 0;
}
}
htmStart(stdout, "GISAID Table View");
cartWarnCatcher(doMiddle, cart, htmlVaWarn);
cartCheckout(&cart);
htmlEnd();
hFreeConn(&conn);
return 0;
}
