void doGsLogin(struct sqlConnection *conn)
/* Process user password post.
* Log into GS
* if successful save gsToken
* else return to login page or to mainpage */
{
char *user = cloneString(cartUsualString(cart, hgtaGsUser, NULL));
char *password = cloneString(cartUsualString(cart, hgtaGsPassword, NULL));
// do not leave them in the cart
cartRemove(cart, hgtaGsUser);
cartRemove(cart, hgtaGsPassword);
if (!(user && password))
errAbort("expecting GenomeSpace user and password");
char *gsToken = getAuthorizationToken(user, password);
if (gsToken)
{
cartSetString(cart, "gsToken", gsToken);
}
else
{
cartRemove(cart, "gsToken");
}
cartSetString(cart, hgtaDoTopSubmit, "get output");
}
static void setDb(struct cartJson *cj, struct hash *paramHash)
/* Set taxId and genome according to db and return the info we'll need to fill in
* the findPosition section. */
{
char *db = cartJsonRequiredParam(paramHash, "db", cj->jw, "setDb");
char *hubUrl = cartJsonOptionalParam(paramHash, "hubUrl");
int taxId = hTaxId(db);
writeFindPositionInfo(cj->jw, db, taxId, hubUrl, hDefaultPos(db));
cartSetString(cart, "db", db);
cartSetString(cart, "position", hDefaultPos(db));
}
void dispatchLocation()
/* When this is called no output has been written at all. We
* look at command variables in cart and figure out if we just
* are going write an HTTP location line, which happens when we
* want to invoke say the genome browser or gene sorter without
* another intermediate page. If we need to do more than that
* then we call hggDoUsualHttp. */
{
struct sqlConnection *conn = NULL;
getDbAndGenome(cart, &database, &genome, oldVars);
setUdcCacheDir();
cartSetString(cart, "db", database); /* Some custom tracks code needs this */
withLabels = cartUsualBoolean(cart, hggLabels, TRUE);
conn = hAllocConn(database);
getGenoGraphs(conn);
/* Handle cases that just want a HTTP Location line: */
if (cartVarExists(cart, hggClickX))
{
clickOnImage(conn);
return;
}
hFreeConn(&conn);
/* For other cases we want to print out some of the usual HTTP
* lines including content-type */
hggDoUsualHttp();
}
static void hubConnectRemakeTrackHubVar(struct cart *cart)
/* Remake trackHub cart variable if need be from various check box vars. */
{
if (cartVarExists(cart, hgHubConnectRemakeTrackHub))
{
struct slPair *hubVarList = cartVarsWithPrefix(cart, hgHubConnectHubVarPrefix);
int prefixLength = strlen(hgHubConnectHubVarPrefix);
struct dyString *trackHubs = dyStringNew(0);
struct slPair *hubVar;
boolean firstOne = TRUE;
for (hubVar = hubVarList; hubVar != NULL; hubVar = hubVar->next)
{
if (cartBoolean(cart, hubVar->name))
{
if (firstOne)
firstOne = FALSE;
else
dyStringAppendC(trackHubs, ' ');
dyStringAppend(trackHubs, hubVar->name + prefixLength);
}
}
slPairFreeList(&hubVarList);
cartSetString(cart, hubConnectTrackHubsVarName, trackHubs->string);
dyStringFree(&trackHubs);
cartRemove(cart, hgHubConnectRemakeTrackHub);
}
}
static void doBigSelectPage(char *db, char *table)
/* Put up big field selection page. Assumes html page open already*/
{
struct joiner *joiner = allJoiner;
struct dbTable *dtList, *dt;
char dbTableBuf[256];
cartSetString(cart, hgtaFieldSelectTable, getDbTable(db, table));
if (strchr(table, '.'))
htmlOpen("Select Fields from %s", table);
else
htmlOpen("Select Fields from %s.%s", db, table);
hPrintf("<FORM NAME=\"mainForm\" ACTION=\"%s\" METHOD=%s>\n", cgiScriptName(),
cartUsualString(cart, "formMethod", "POST"));
cartSaveSession(cart);
cgiMakeHiddenVar(hgtaDatabase, db);
cgiMakeHiddenVar(hgtaTable, table);
dbOverrideFromTable(dbTableBuf, &db, &table);
showTableFields(db, table, TRUE);
dtList = extraTableList(selFieldLinkedTablePrefix());
showLinkedFields(dtList);
dt = dbTableNew(db, table);
slAddHead(&dtList, dt);
showLinkedTables(joiner, dtList, selFieldLinkedTablePrefix(),
hgtaDoSelectFieldsMore, "allow selection from checked tables");
/* clean up. */
hPrintf("</FORM>");
cgiDown(0.9);
htmlClose();
joinerFree(&joiner);
}
void doAdvFilterKeyPasted(struct sqlConnection *conn, struct column *colList,
struct column *col)
/* Handle submission in key-paste in form. */
{
char *pasteVarName = colVarName(col, keyWordPastedPrefix);
char *pasteVal = trimSpaces(cartString(cart, pasteVarName));
char *keyVarName = advFilterName(col, "keyFile");
if (pasteVal == NULL || pasteVal[0] == 0)
{
/* If string is empty then clear cart variable. */
cartRemove(cart, keyVarName);
}
else
{
/* Else write variable to temp file and save temp
* file name. */
struct tempName tn;
FILE *f;
makeTempName(&tn, "near", ".key");
f = mustOpen(tn.forCgi, "w");
mustWrite(f, pasteVal, strlen(pasteVal));
carefulClose(&f);
cartSetString(cart, keyVarName, tn.forCgi);
}
cartRemovePrefix(cart, keyWordPastedPrefix);
doAdvFilter(conn, colList);
}
void doMiddle(struct cart *theCart)
/* Write header and body of html page. */
{
char *userSeq;
char *db, *organism;
boolean clearUserSeq = cgiBoolean("Clear");
cart = theCart;
dnaUtilOpen();
orgChange = sameOk(cgiOptionalString("changeInfo"),"orgChange");
if (orgChange)
{
cgiVarSet("db", hDefaultDbForGenome(cgiOptionalString("org")));
}
getDbAndGenome(cart, &db, &organism, oldVars);
char *oldDb = cloneString(db);
findClosestServer(&db, &organism);
/* Get sequence - from userSeq variable, or if
* that is empty from a file. */
if (clearUserSeq)
{
cartSetString(cart, "userSeq", "");
cartSetString(cart, "seqFile", "");
}
userSeq = cartUsualString(cart, "userSeq", "");
if (isEmpty(userSeq))
{
userSeq = cartOptionalString(cart, "seqFile");
}
if (isEmpty(userSeq) || orgChange)
{
cartWebStart(theCart, db, "%s BLAT Search", trackHubSkipHubName(organism));
if (differentString(oldDb, db))
printf("<HR><P><EM><B>Note:</B> BLAT search is not available for %s %s; "
"defaulting to %s %s</EM></P><HR>\n",
hGenome(oldDb), hFreezeDate(oldDb), organism, hFreezeDate(db));
askForSeq(organism,db);
cartWebEnd();
}
else
{
blatSeq(skipLeadingSpaces(userSeq), organism);
}
}
static void setTaxId(struct cartJson *cj, struct hash *paramHash)
/* Set db and genome according to taxId (and/or db) and return the info we'll need
* to fill in the findPosition section. */
{
char *taxIdStr = cartJsonRequiredParam(paramHash, "taxId", cj->jw, "setTaxId");
char *db = cartJsonOptionalParam(paramHash, "db");
int taxId = atoi(taxIdStr);
if (isEmpty(db))
db = hDbForTaxon(taxId);
if (isEmpty(db))
jsonWriteStringf(cj->jw, "error", "No db for taxId '%s'", taxIdStr);
else
{
writeFindPositionInfo(cj->jw, db, taxId, NULL, hDefaultPos(db));
cartSetString(cart, "db", db);
cartSetString(cart, "position", hDefaultPos(db));
}
}
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");
}
char *hubConnectLoadHubs(struct cart *cart)
/* load the track data hubs. Set a static global to remember them */
{
char *newDatabase = checkForNew( cart);
cartSetString(cart, hgHubConnectRemakeTrackHub, "on");
struct hubConnectStatus *hubList = hubConnectStatusListFromCart(cart);
globalHubList = hubList;
return newDatabase;
}
static void setCheckVarsForTable(char *dbTable, char *val)
/* Return list of check variables for this table. */
{
char prefix[128];
struct hashEl *varList, *var;
safef(prefix, sizeof(prefix), "%s%s.", checkVarPrefix(), dbTable);
varList = cartFindPrefix(cart, prefix);
for (var = varList; var != NULL; var = var->next)
cartSetString(cart, var->name, val);
hashElFreeList(&varList);
}
void copyCartVars(struct cart *cart, char **source, char **dest, int count)
/* Copy from source to dest. */
{
int i;
for (i=0; i<count; ++i)
{
char *s = cartOptionalString(cart, source[i]);
if (s != NULL)
cartSetString(cart, dest[i], s);
else
cartRemove(cart, dest[i]);
}
}
void writePcrResultTrack(struct gfPcrOutput *gpoList, char *db, char *target)
/* Write trash files and store their name in a cart variable. */
{
char *cartVar = pcrResultCartVar(db);
struct tempName bedTn, primerTn;
char buf[2048];
trashDirFile(&bedTn, "hgPcr", "hgPcr", ".psl");
trashDirFile(&primerTn, "hgPcr", "hgPcr", ".txt");
gfPcrOutputWriteAll(gpoList, "psl", NULL, bedTn.forCgi);
writePrimers(gpoList, primerTn.forCgi);
if (isNotEmpty(target))
safef(buf, sizeof(buf), "%s %s %s", bedTn.forCgi, primerTn.forCgi, target);
else
safef(buf, sizeof(buf), "%s %s", bedTn.forCgi, primerTn.forCgi);
cartSetString(cart, cartVar, buf);
}
static void setIfUnset(struct cartJson *cj, struct hash *paramHash)
/* For each name in paramHash, if that cart variable doesn't already have a non-empty
* value, set it to the value. */
{
struct hashCookie cookie = hashFirst(paramHash);
struct hashEl *hel;
while ((hel = hashNext(&cookie)) != NULL)
{
if (isEmpty(cartOptionalString(cj->cart, hel->name)))
{
char *val = jsonStringVal((struct jsonElement *)(hel->val), hel->name);
if (val)
cartSetString(cj->cart, hel->name, val);
}
}
}
static struct hubConnectStatus *getAndSetHubStatus( struct cart *cart, char *url,
boolean set)
/* make sure url is in hubStatus table, fetch the hub to get latest
* labels and db information.
* Set the cart variable to turn the hub on if set == TRUE.
*/
{
char *errorMessage = NULL;
unsigned id;
/* first see if url is in hubStatus table */
if ((id = getHubId(url, &errorMessage)) == 0)
{
/* the url is not in the hubStatus table, add it */
insertHubUrlInStatus(url);
if ((id = getHubId(url, &errorMessage)) == 0)
{
errAbort("opened hub, but could not get it out of the hubStatus table");
}
}
/* allocate a hub */
struct hubConnectStatus *hub = NULL;
AllocVar(hub);
hub->id = id;
hub->hubUrl = cloneString(url);
/* new fetch the contents of the hub to fill in the status table */
struct trackHub *tHub = fetchHub( hub, &errorMessage);
if (tHub != NULL)
hub->trackHub = tHub;
/* update the status table with the lastest label and database information */
hubUpdateStatus( errorMessage, hub);
/* if we're turning on the hub, set the cart variable */
if (set)
{
char hubName[32];
safef(hubName, sizeof(hubName), "%s%u", hgHubConnectHubVarPrefix, id);
cartSetString(cart, hubName, "1");
}
return hub;
}
void doId(struct sqlConnection *conn)
/* Set up Gene Pix on given ID. */
{
int id = cartInt(cart, hgpDoId);
struct slName *genes = visiGeneGeneName(conn, id);
if (genes == NULL)
{
cartRemove(cart, hgpListSpec);
cartRemove(cart, hgpId);
}
else
{
cartSetInt(cart, hgpId, id);
cartSetString(cart, hgpListSpec, genes->name);
}
slFreeList(&genes);
doDefault(conn, FALSE);
}
void userSettingsUseNamed(struct userSettings *us, char *setName)
/* Use named collection of settings. */
{
struct cart *cart = us->cart;
char *varName = settingsVarName(us->savePrefix, setName);
char *settings = cartOptionalString(cart, varName);
if (settings != NULL)
{
struct hash *hash = hashVarLine(settings, 1);
struct hashEl *list = hashElListHash(hash);
struct hashEl *el;
for (el = list; el != NULL; el = el->next)
cartSetString(cart, el->name, el->val);
slFreeList(&list);
hashFree(&hash);
}
freez(&varName);
}
static void activatePslTrackIfCgi(struct track *tg)
/* the publications hgc creates links back to the browser with
* the cgi param pubsFilterArticleId to show only a single type
* of feature for the pubsBlatPsl track.
* If the parameter was supplied, we save it here
* into the cart and activate the track.
*/
{
char *articleId = cgiOptionalString(PUBSFILTERNAME);
//if (articleId==NULL)
//articleId = cartOptionalString(cart, PUBSFILTERNAME);
if (articleId!=NULL)
{
cartSetString(cart, PUBSFILTERNAME, articleId);
tdbSetCartVisibility(tg->tdb, cart, hCarefulTrackOpenVis(database, tg->track));
tg->visibility=tvPack;
}
}
static void saveSettings(struct userSettings *us, char *varName)
/* Save captured settings to varName. */
{
struct cart *cart = us->cart;
struct slName *capture;
struct dyString *dy = dyStringNew(4*1024);
for (capture = us->saveList; capture != NULL; capture = capture->next)
{
char *name = capture->name;
char *val = cartOptionalString(cart, name);
if (val != NULL)
{
dyStringPrintf(dy, "%s=", name);
dyStringAppendQuoted(dy, val);
}
}
cartSetString(cart, varName, dy->string);
dyStringFree(&dy);
}
static char * outMafTableDrop(struct cart *cart, struct sqlConnection *conn)
{
struct slName *list = hTrackTablesOfType(conn, "wigMaf%%");
int count = slCount(list);
if (count == 0)
errAbort("There are no multiple alignments available for this genome.");
char **tables = needMem(sizeof(char *) * count);
char **tb = tables;
char *mafTable = cartOptionalString(cart, hgtaCGIGeneMafTable);
if (mafTable != NULL)
{
struct slName *l = list;
for(; l; l=l->next)
if (sameString(l->name, mafTable))
break;
/* didn't find mafTable in list, reset it */
if (l == NULL)
mafTable = NULL;
}
if (mafTable == NULL)
{
if ((mafTable = getConservationTrackName(conn)) == NULL)
mafTable = list->name;
cartSetString(cart, hgtaCGIGeneMafTable, mafTable);
}
for(; list; list = list->next)
*tb++ = list->name;
printf("<B>MAF table: </B>\n");
cgiMakeDropListFull(hgtaCGIGeneMafTable, tables, tables,
count , mafTable, onChangeGenome());
return mafTable;
}
static void changePosition(struct cartJson *cj, char *newPosition)
/* Update position in cart, after performing lookup if necessary.
* Usually we don't report what we just changed, but since we might modify it,
* print out the final value. */
{
char *db = cartString(cj->cart, "db");
char *chrom = NULL;
int start=0, end=0;
struct hgPositions *hgp = genomePosCJ(cj->jw, db, newPosition, &chrom, &start, &end, cj->cart);
// If it resolved to a single position, update the cart; otherwise the app can
// present the error (or list of matches) to the user.
if (hgp && hgp->singlePos)
{
char newPosBuf[128];
safef(newPosBuf, sizeof(newPosBuf), "%s:%d-%d", chrom, start+1, end);
cartSetString(cj->cart, "position", newPosBuf);
jsonWriteString(cj->jw, "position", newPosBuf);
}
else
// Search failed; restore position from cart
jsonWriteString(cj->jw, "position", cartUsualString(cj->cart, "position", hDefaultPos(db)));
}
struct hvGfx *oneTrackMakeTrackHvg(char *trackName, char *gifName)
/* Set up a single track, load it, draw it and return the graphics object: */
{
char *visStr = cloneString(
cartUsualString(cart, trackName, hTrackOpenVis(trackName)) );
cartSetString(cart, trackName, visStr);
struct trackDb *tdb = hTrackDbForTrack(trackName);
tdbSortPrioritiesFromCart(cart, &tdb);
if(tdb->subtracks)
tdbSortPrioritiesFromCart(cart, &(tdb->subtracks));
struct track *tg = trackFromTrackDb(tdb);
tg->visibility = hTvFromString(visStr);
trackList = tg;
tg->loadItems(tg);
limitVisibility(tg);
int height = tg->totalHeight(tg, tg->limitedVis);
struct hvGfx *hvg = hvGfxOpenGif(insideWidth, height, gifName, TRUE);
initColors(hvg);
findTrackColors(hvg, tg);
/* This is the only image we'll draw, so offset=(0,0). */
int xOff = 0, yOff = 0;
MgFont *font = tl.font;
hvGfxSetClip(hvg, xOff, yOff, insideWidth, tg->height);
tg->drawItems(tg, winStart, winEnd, hvg, xOff, yOff, insideWidth, font,
hvGfxFindRgb(hvg, &tg->color), tg->limitedVis);
/* MEMORY LEAK -- Freeing items slows hgTracks down unacceptably so we
* don't do it, and it has become vestigial. For example, wigFreeItems
* is a no-op because the author noted that it is never invoked. */
#ifdef SLOW
tg->freeItems(tg);
#endif /* SLOW */
return hvg;
}
void loadAffyTranscriptome(struct track *tg)
/* Convert sample info in window to linked feature. */
{
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char **row;
int rowOffset;
struct sample *sample;
struct linkedFeatures *lfList = NULL, *lf;
char *hasDense = NULL;
char *where = NULL;
char query[256];
char tableName[256];
int zoom1 = 23924, zoom2 = 2991; /* bp per data point */
float pixPerBase = 0;
/* Set it up so we don't have linear interpretation.. */
char *noLinearInterpString = wiggleEnumToString(wiggleNoInterpolation);
cartSetString(cart, "affyTranscriptome.linear.interp", noLinearInterpString);
if(tl.picWidth == 0)
errAbort("hgTracks.c::loadAffyTranscriptome() - can't have pixel width of 0");
pixPerBase = (winEnd - winStart)/ tl.picWidth;
/* Determine zoom level. */
if(pixPerBase >= zoom1)
safef(tableName, sizeof(tableName), "%s_%s", "zoom1", tg->table);
else if(pixPerBase >= zoom2)
safef(tableName, sizeof(tableName), "%s_%s", "zoom2", tg->table);
else
safef(tableName, sizeof(tableName), "%s", tg->table);
/*see if we have a summary table*/
if(hTableExists(database, tableName))
safef(query, sizeof(query), "select name from %s where name = '%s' limit 1", tableName, tg->shortLabel);
else
{
warn("<p>Couldn't find table %s<br><br>", tableName);
safef(query, sizeof(query), "select name from %s where name = '%s' limit 1", tg->table, tg->shortLabel);
safef(tableName, sizeof(tableName), "%s", tg->table);
}
hasDense = sqlQuickQuery(conn, query, query, sizeof(query));
/* If we're in dense mode and have a summary table load it. */
if(tg->visibility == tvDense)
{
if(hasDense != NULL)
{
safef(query, sizeof(query), " name = '%s' ", tg->shortLabel);
where = cloneString(query);
}
}
sr = hRangeQuery(conn, tableName, chromName, winStart, winEnd, where, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
sample = sampleLoad(row+rowOffset);
lf = lfFromSample(sample);
slAddHead(&lfList, lf);
sampleFree(&sample);
}
if(where != NULL)
freez(&where);
sqlFreeResult(&sr);
hFreeConn(&conn);
slReverse(&lfList);
/* sort to bring items with common names to the same line
but only for tracks with a summary table (with name=shortLabel) in
dense mode*/
if( hasDense != NULL )
{
sortGroupList = tg; /* used to put track name at top of sorted list. */
slSort(&lfList, lfNamePositionCmp);
sortGroupList = NULL;
}
tg->items = lfList;
}
static void doMainPage()
/* Send HTML with javascript to bootstrap the user interface. */
{
// Start web page with new banner
char *db = NULL, *genome = NULL, *clade = NULL;
getDbGenomeClade(cart, &db, &genome, &clade, oldVars);
// If CGI has &lastDbPos=..., handle that here and save position to cart so it's in place for
// future cartJson calls.
char *position = cartGetPosition(cart, db, NULL);
cartSetString(cart, "position", position);
webStartJWest(cart, db, "Genome Browser Gateway");
if (cgiIsOnWeb())
checkForGeoMirrorRedirect(cart);
#define WARNING_BOX_START "<div id=\"previewWarningRow\" class=\"jwRow\">" \
"<div id=\"previewWarningBox\" class=\"jwWarningBox\">"
#define UNDER_DEV "Data and tools on this site are under development, have not been reviewed " \
"for quality, and are subject to change at any time. "
#define MAIN_SITE "The high-quality, reviewed public site of the UCSC Genome Browser is " \
"available for use at <a href=\"http://genome.ucsc.edu/\">http://genome.ucsc.edu/</a>."
#define WARNING_BOX_END "</div></div>"
if (hIsPreviewHost())
{
puts(WARNING_BOX_START
"WARNING: This is the UCSC Genome Browser preview site. "
"This website is a weekly mirror of our internal development server for public access. "
UNDER_DEV
"We provide this site for early access, with the warning that it is less available "
"and stable than our public site. "
MAIN_SITE
WARNING_BOX_END);
}
if (hIsPrivateHost() && !hHostHasPrefix("hgwdev-demo6"))
{
puts(WARNING_BOX_START
"WARNING: This is the UCSC Genome Browser development site. "
"This website is used for testing purposes only and is not intended for general public "
"use. "
UNDER_DEV
MAIN_SITE
WARNING_BOX_END);
}
// The visible page elements are all in ./hgGateway.html, which is transformed into a quoted .h
// file containing a string constant that we #include and print here (see makefile).
puts(
#include "hgGateway.html.h"
);
// Set global JS variables hgsid, activeGenomes, and survey* at page load time
// We can't just use "var hgsid = " or the other scripts won't see it -- it has to be
// "window.hgsid = ".
puts("<script>");
printf("window.%s = '%s';\n", cartSessionVarName(), cartSessionId(cart));
puts("window.activeGenomes =");
printActiveGenomes();
puts(";");
char *surveyLink = cfgOption("survey");
if (isNotEmpty(surveyLink) && !sameWord(surveyLink, "off"))
{
printf("window.surveyLink=\"%s\";\n", jsonStringEscape(surveyLink));
char *surveyLabel = cfgOptionDefault("surveyLabel", "Please take our survey");
printf("window.surveyLabel=\"%s\";\n", jsonStringEscape(surveyLabel));
char *surveyLabelImage = cfgOption("surveyLabelImage");
if (isNotEmpty(surveyLabelImage))
printf("window.surveyLabelImage=\"%s\";\n", jsonStringEscape(surveyLabelImage));
else
puts("window.surveyLabelImage=null;");
}
else
{
puts("window.surveyLink=null;");
puts("window.surveyLabel=null;");
puts("window.surveyLabelImage=null;");
}
puts("</script>");
puts("<script src=\"../js/es5-shim.4.0.3.min.js\"></script>");
puts("<script src=\"../js/es5-sham.4.0.3.min.js\"></script>");
puts("<script src=\"../js/lodash.3.10.0.compat.min.js\"></script>");
puts("<script src=\"../js/cart.js\"></script>");
webIncludeResourceFile("jquery-ui.css");
jsIncludeFile("jquery-ui.js", NULL);
jsIncludeFile("jquery.watermarkinput.js", NULL);
jsIncludeFile("utils.js",NULL);
// Phylogenetic tree .js file, produced by dbDbTaxonomy.pl:
char *dbDbTree = cfgOptionDefault("hgGateway.dbDbTaxonomy", "../js/dbDbTaxonomy.js");
if (isNotEmpty(dbDbTree))
printf("<script src=\"%s\"></script>\n", dbDbTree);
// Main JS for hgGateway:
puts("<script src=\"../js/hgGateway.js\"></script>");
webIncludeFile("inc/jWestFooter.html");
cartFlushHubWarnings();
webEndJWest();
}
void sortGenes(struct sqlConnection *conn)
/* Put up sort gene page. */
{
cartWebStart(cart, database, "Finding Candidate Genes for Gene Sorter");
if (!hgNearOk(database))
errAbort("Sorry, gene sorter not available for this database.");
/* Get list of regions. */
struct genoGraph *gg = ggFirstVisible();
double threshold = getThreshold();
struct bed3 *bed, *bedList = regionsOverThreshold(gg);
/* Figure out what table and column are the sorter's main gene set. */
struct hash *genomeRa = hgReadRa(genome, database, "hgNearData",
"genome.ra", NULL);
char *geneTable = hashMustFindVal(genomeRa, "geneTable");
char *idColumn = hashMustFindVal(genomeRa, "idColumn");
/* if marker labels were present when the file was uploaded, they are saved here */
char cgmName[256];
safef(cgmName, sizeof(cgmName), "%s.cgm", gg->binFileName);
struct lineFile *m = lineFileMayOpen(cgmName, TRUE);
char *cgmRow[4];
cgmRow[0] = ""; /* dummy row */
cgmRow[1] = "";
cgmRow[2] = "0";
cgmRow[3] = "0";
FILE *g = NULL;
int markerCount = 0;
struct tempName snpTn;
if (m)
{
/* Create custom column output file. */
trashDirFile(&snpTn, "hgg", "marker", ".mrk");
g = mustOpen(snpTn.forCgi, "w");
fprintf(g,
"column name=\"%s Markers\" shortLabel=\"%s Markers over threshold\" longLabel=\"%s Markers in regions over threshold\" "
"visibility=on priority=99 "
"\n"
, gg->shortLabel
, gg->shortLabel
, gg->shortLabel
);
}
/*** Build up hash of all transcriptHash that are in region. */
struct hash *transcriptHash = hashNew(16);
/* This loop handles one chromosome at a time. It depends on
* the bedList being sorted by chromosome. */
for (bed = bedList; bed != NULL; )
{
/* Make binKeeper and stuff in all regions in this chromosome into it. */
char *chrom = bed->chrom;
int chromSize = hChromSize(database, chrom);
struct binKeeper *bk = binKeeperNew(0, chromSize);
while (bed != NULL && sameString(chrom, bed->chrom))
{
binKeeperAdd(bk, bed->chromStart, bed->chromEnd, bed);
bed = bed->next;
}
struct binKeeper *bkGenes = NULL;
if (m)
bkGenes = binKeeperNew(0, chromSize);
/* Query database to find out bounds of all genes on this chromosome
* and if they overlap any of the regions then put them in the hash. */
char query[512];
safef(query, sizeof(query),
"select name,txStart,txEnd from %s where chrom='%s'", geneTable, chrom);
struct sqlResult *sr = sqlGetResult(conn, query);
char **row;
while ((row = sqlNextRow(sr)) != NULL)
{
char *name = row[0];
int start = sqlUnsigned(row[1]);
int end = sqlUnsigned(row[2]);
if (binKeeperAnyOverlap(bk, start, end))
{
hashStore(transcriptHash, name);
if (m)
binKeeperAdd(bkGenes, start, end, cloneString(name));
}
}
sqlFreeResult(&sr);
if (m)
{
/* Read cgm file if it exists, looking at all markers on this chromosome
* and if they overlap any of the regions and genes then output them. */
do
{
// marker, chrom, chromStart, val
char *marker = cgmRow[0];
char *chr = cgmRow[1];
int start = sqlUnsigned(cgmRow[2]);
int end = start+1;
double val = sqlDouble(cgmRow[3]);
int cmp = strcmp(chr,chrom);
if (cmp > 0)
break;
if (cmp == 0)
{
if (val >= threshold)
{
struct binElement *el, *bkList = binKeeperFind(bkGenes, start, end);
for (el = bkList; el; el=el->next)
{
/* output to custom column trash file */
fprintf(g, "%s %s\n", (char *)el->val, marker);
}
if (bkList)
{
++markerCount;
slFreeList(&bkList);
}
}
}
}
while (lineFileRow(m, cgmRow));
}
/* Clean up for this chromosome. */
binKeeperFree(&bk);
if (m)
{
/* For speed, we do not free up the values (cloned the kg names earlier) */
binKeeperFree(&bkGenes);
}
}
/* Get list of all transcripts in regions. */
struct hashEl *el, *list = hashElListHash(transcriptHash);
/* Create file with all matching gene IDs. */
struct tempName keyTn;
trashDirFile(&keyTn, "hgg", "key", ".key");
FILE *f = mustOpen(keyTn.forCgi, "w");
for (el = list; el != NULL; el = el->next)
fprintf(f, "%s\n", el->name);
carefulClose(&f);
/* Print out some info. */
hPrintf("Thresholding <i>%s</i> at %g. ", gg->shortLabel, threshold);
hPrintf("There are %d regions covering %lld bases.<BR>\n",
slCount(bedList), bedTotalSize((struct bed*)bedList) );
hPrintf("Installed a Gene Sorter filter that selects only genes in these regions.<BR>\n");
if (m)
{
hPrintf("There are %d markers in the regions over threshold that overlap knownGenes.<BR>\n", markerCount);
hPrintf("Installed a Gene Sorter custom column called \"%s Markers\" with these markers.<BR>\n", gg->shortLabel);
}
/* close custom column output file */
if (m)
{
lineFileClose(&m);
carefulClose(&g);
}
/* Stuff cart variable with name of file. */
char keyCartName[256];
safef(keyCartName, sizeof(keyCartName), "%s%s.keyFile",
advFilterPrefix, idColumn);
cartSetString(cart, keyCartName, keyTn.forCgi);
cartSetString(cart, customFileVarName, snpTn.forCgi);
char snpVisCartNameTemp[256];
char *snpVisCartName = NULL;
safef(snpVisCartNameTemp, sizeof(snpVisCartNameTemp), "%s%s Markers.vis",
colConfigPrefix, gg->shortLabel);
snpVisCartName = replaceChars(snpVisCartNameTemp, " ", "_");
cartSetString(cart, snpVisCartName, "1");
freeMem(snpVisCartName);
hPrintf("<FORM ACTION=\"../cgi-bin/hgNear\" METHOD=GET>\n");
cartSaveSession(cart);
hPrintf("<CENTER>");
cgiMakeButton("submit", "go to gene sorter");
hPrintf("</CENTER>");
hPrintf("</FORM>");
cartWebEnd();
}
void saveSubjList(struct subjInfo *subjListIn)
/* save the filtered list of subject gisaids to a file for other applications to use */
{
struct subjInfo *subjList;
char *outName = cartOptionalString(cart, gisaidSubjList);
char *outName2= cartOptionalString(cart, gisaidSeqList);
char *outName3= cartOptionalString(cart, gisaidAaSeqList);
char *outNameTemp;
struct tempName tn;
struct tempName tn2;
struct tempName tn3;
struct tempName tnTemp;
struct sqlResult *sr;
char **row;
char query[255];
int cnt;
char cmd[512];
if (!outName)
{
trashDirFile(&tn, "ct", "gisaidSubj", ".list");
outName = tn.forCgi;
}
if (!outName2)
{
trashDirFile(&tn2, "ct", "gisaidSeq", ".list");
outName2 = tn2.forCgi;
}
if (!outName3)
{
trashDirFile(&tn3, "ct", "gisaidAaSeq", ".list");
outName3 = tn3.forCgi;
}
trashDirFile(&tnTemp, "ct", "gisaidListTemp", ".list");
outNameTemp = tnTemp.forCgi;
FILE *outF = mustOpen(outName,"w");
FILE *outF2= mustOpen(outName2,"w");
FILE *outF3= mustOpen(outName3,"w");
cnt = 0;
subjList = subjListIn;
while (subjList)
{
fprintf(outF, "%s\n", subjList->fields[1]);
sqlSafef(query, sizeof(query),
"select distinct seqId from h1n1SeqXref where islId='%s'",
subjList->fields[0]);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
/* Remove "ss." from the front of the DNA sequence ID,
so that they could be used both for DNA and protein MSA maf display */
fprintf(outF2, "%s\t%s\n", row[0], subjList->fields[1]);
cnt++;
}
sqlFreeResult(&sr);
subjList=subjList->next;
}
subjList = subjListIn;
while (subjList)
{
fprintf(outF, "%s\n", subjList->fields[0]);
sqlSafef(query, sizeof(query),
"select distinct seqId, geneSymbol from h1n1SeqXref where islId='%s'",
subjList->fields[0]);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
/* Remove "ss." from the front of the DNA sequence ID,
so that they could be used both for DNA and protein MSA maf display */
fprintf(outF3, "%s_%s\t%s\n", row[0], row[1], subjList->fields[1]);
cnt++;
}
sqlFreeResult(&sr);
subjList=subjList->next;
}
carefulClose(&outF);
carefulClose(&outF2);
carefulClose(&outF3);
/* sort -u to make the selection lists unique */
sprintf(cmd, "cat %s |sort -u >%s", outName, outNameTemp);
system(cmd);
sprintf(cmd, "mv %s %s", outNameTemp, outName);
system(cmd);
sprintf(cmd, "cat %s |sort -u >%s", outName2, outNameTemp);
system(cmd);
sprintf(cmd, "mv %s %s", outNameTemp, outName2);
system(cmd);
sprintf(cmd, "cat %s |sort -u >%s", outName3, outNameTemp);
system(cmd);
sprintf(cmd, "mv %s %s", outNameTemp, outName3);
system(cmd);
cartSetString(cart, gisaidSubjList, outName);
cartSetString(cart, gisaidSeqList, outName2);
cartSetString(cart, gisaidAaSeqList, outName3);
}
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 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 getDbGenomeClade(struct cart *cart, char **retDb, char **retGenome,
char **retClade, struct hash *oldVars)
/* Examine CGI and cart variables to determine which db, genome, or clade
* has been selected, and then adjust as necessary so that all three are
* consistent. Detect changes and reset db-specific cart variables.
* Save db, genome and clade in the cart so it will be consistent hereafter.
* The order of preference here is as follows:
* If we got a request that explicitly names the db, that takes
* highest priority, and we synch the organism to that db.
* If we get a cgi request for a specific organism then we use that
* organism to choose the DB. If just clade, go from there.
* In the cart only, we use the same order of preference.
* If someone requests an Genome we try to give them the same db as
* was in their cart, unless the Genome doesn't match.
*/
{
boolean gotClade = hGotClade();
*retDb = cgiOptionalString(dbCgiName);
*retGenome = cgiOptionalString(orgCgiName);
*retClade = cgiOptionalString(cladeCgiName);
/* phoneHome business */
phoneHome();
/* Was the database passed in as a cgi param?
* If so, it takes precedence and determines the genome. */
if (*retDb && hDbExists(*retDb))
{
*retGenome = hGenome(*retDb);
}
/* If no db was passed in as a cgi param then was the organism (a.k.a. genome)
* passed in as a cgi param?
* If so, the we use the proper database for that genome. */
else if (*retGenome && !sameWord(*retGenome, "0"))
{
*retDb = getDbForGenome(*retGenome, cart);
*retGenome = hGenome(*retDb);
}
else if (*retClade && gotClade)
{
*retGenome = hDefaultGenomeForClade(*retClade);
*retDb = getDbForGenome(*retGenome, cart);
}
/* If no cgi params passed in then we need to inspect the session */
else
{
*retDb = cartOptionalString(cart, dbCgiName);
*retGenome = cartOptionalString(cart, orgCgiName);
*retClade = cartOptionalString(cart, cladeCgiName);
/* If there was a db found in the session that determines everything. */
if (*retDb && hDbExists(*retDb))
{
*retGenome = hGenome(*retDb);
}
else if (*retGenome && !sameWord(*retGenome, "0"))
{
*retDb = hDefaultDbForGenome(*retGenome);
}
else if (*retClade && gotClade)
{
*retGenome = hDefaultGenomeForClade(*retClade);
*retDb = getDbForGenome(*retGenome, cart);
}
/* If no organism in the session then get the default db and organism. */
else
{
*retDb = hDefaultDb();
*retGenome = hGenome(*retDb);
}
}
*retDb = cloneString(*retDb);
*retGenome = cloneString(*retGenome);
*retClade = hClade(*retGenome);
/* Detect change of database and reset db-specific cart variables: */
if (oldVars)
{
char *oldDb = hashFindVal(oldVars, "db");
char *oldOrg = hashFindVal(oldVars, "org");
char *oldClade = hashFindVal(oldVars, "clade");
if ((!IS_CART_VAR_EMPTY(oldDb) && differentWord(oldDb, *retDb)) ||
(!IS_CART_VAR_EMPTY(oldOrg) && differentWord(oldOrg, *retGenome)) ||
(!IS_CART_VAR_EMPTY(oldClade) && differentWord(oldClade, *retClade)))
{
/* Change position to default -- unless it was passed in via CGI: */
if (cgiOptionalString("position") == NULL)
cartSetString(cart, "position", hDefaultPos(*retDb));
/* hgNear search term -- unless it was passed in via CGI: */
if (cgiOptionalString("near_search") == NULL)
cartRemove(cart, "near_search");
/* hgBlat results (hgUserPsl track): */
cartRemove(cart, "ss");
/* hgTables correlate: */
cartRemove(cart, "hgta_correlateTrack");
cartRemove(cart, "hgta_correlateTable");
cartRemove(cart, "hgta_correlateGroup");
cartRemove(cart, "hgta_correlateOp");
cartRemove(cart, "hgta_nextCorrelateTrack");
cartRemove(cart, "hgta_nextCorrelateTable");
cartRemove(cart, "hgta_nextCorrelateGroup");
cartRemove(cart, "hgta_nextCorrelateOp");
cartRemove(cart, "hgta_corrWinSize");
cartRemove(cart, "hgta_corrMaxLimitCount");
}
}
/* Save db, genome (as org) and clade in cart. */
cartSetString(cart, "db", *retDb);
cartSetString(cart, "org", *retGenome);
if (gotClade)
cartSetString(cart, "clade", *retClade);
}
static void wiggleLinkedFeaturesDraw(struct track *tg,
int seqStart, int seqEnd,
struct hvGfx *hvg, int xOff, int yOff, int width,
MgFont *font, Color color, enum trackVisibility vis)
/* Currently this routine is adapted from Terry's
* linkedFeatureSeriesDraw() routine.
* It is called for 'sample' tracks as specified in the trackDb.ra.
* and it looks at the cart to decide whether to interpolate, fill blocks,
* and use anti-aliasing.*/
{
int i;
struct linkedFeatures *lf;
struct simpleFeature *sf;
int y = yOff;
int heightPer = tg->heightPer;
int lineHeight = tg->lineHeight;
int x1,x2;
boolean isFull = (vis == tvFull);
Color bColor = tg->ixAltColor;
double scale = scaleForPixels(width);
int prevX = -1;
int gapPrevX = -1;
double prevY = -1;
double y1 = -1, y2;
int ybase;
int sampleX, sampleY; /* A sample in sample coordinates.
* Sample X coordinate is chromosome coordinate.
* Sample Y coordinate is usually 0-1000 */
int binCount = 1.0/tg->scaleRange; /* Maximum sample Y coordinate. */
int bin; /* Sample Y coordinates are first converted to
* bin coordinates, and then to pixels. I'm not
* totally sure why. */
int currentX, currentXEnd, currentWidth;
int leftSide, rightSide;
int noZoom = 1;
enum wiggleOptEnum wiggleType;
char *interpolate = NULL;
char *aa = NULL;
boolean antiAlias = FALSE;
int fill;
int lineGapSize;
double min0, max0;
char o1[128]; /* Option 1 - linear interp */
char o2[128]; /* Option 2 - anti alias */
char o3[128]; /* Option 3 - fill */
char o4[128]; /* Option 4 - minimum vertical range cutoff of plot */
char o5[128]; /* Option 5 - maximum vertical range cutoff of plot */
char o6[128]; /* Option 6 - max gap where interpolation is still done */
char cartStr[64];
char *fillStr;
double hFactor;
double minRange, maxRange;
double minRangeCutoff, maxRangeCutoff;
Color gridColor = hvGfxFindRgb(hvg, &guidelineColor); /* for horizontal lines*/
lf=tg->items;
if(lf==NULL) return;
//take care of cart options
safef( o1, 128,"%s.linear.interp", tg->track);
safef( o2, 128, "%s.anti.alias", tg->track);
safef( o3, 128,"%s.fill", tg->track);
safef( o4, 128,"%s.min.cutoff", tg->track);
safef( o5, 128,"%s.max.cutoff", tg->track);
safef( o6, 128,"%s.interp.gap", tg->track);
interpolate = cartUsualString(cart, o1, "Linear Interpolation");
wiggleType = wiggleStringToEnum(interpolate);
aa = cartUsualString(cart, o2, "on");
antiAlias = sameString(aa, "on");
//don't fill gcPercent track by default (but fill others)
if(sameString( tg->table, "pGC") && sameString(database,"zooHuman3"))
{
fillStr = cartUsualString(cart, o3, "0");
}
else
{
fillStr = cartUsualString(cart, o3, "1");
}
fill = atoi(fillStr);
cartSetString(cart, o3, fillStr );
//the 0.1 is so the label doesn't get truncated with integer valued user input min
//display range.
minRangeCutoff = max( atof(cartUsualString(cart,o4,"0.0"))-0.1, tg->minRange );
maxRangeCutoff = min( atof(cartUsualString(cart,o5,"1000.0"))+0.1, tg->maxRange);
lineGapSize = atoi(cartUsualString(cart, o6, "200"));
//update cart settings to reflect truncated range cutoff values
cartSetString( cart, "win", "F" );
safef( cartStr, 64, "%g", minRangeCutoff );
cartSetString( cart, o4, cartStr );
safef( cartStr, 64, "%g", maxRangeCutoff );
cartSetString( cart, o5, cartStr );
heightPer = tg->heightPer+1;
hFactor = (double)heightPer*tg->scaleRange;
//errAbort( "min=%g, max=%g\n", minRangeCutoff, maxRangeCutoff );
if( sameString( tg->table, "zoo" ) || sameString( tg->table, "zooNew" ) )
binCount = binCount - 100; //save some space at top, between each zoo species
minRange = whichSampleBin( minRangeCutoff, tg->minRange, tg->maxRange, binCount );
maxRange = whichSampleBin( maxRangeCutoff, tg->minRange, tg->maxRange, binCount );
//errAbort( "(%g,%g) cutoff=(%g,%g)\n", tg->minRange, tg->maxRange, minRangeCutoff, maxRangeCutoff );
if( sameString( tg->table, "zoo" ) || sameString( tg->table, "zooNew" ) )
{
/*Always interpolate zoo track (since gaps are explicitly defined*/
lineGapSize = -1;
}
else if( tg->minRange == 0 && tg->maxRange == 8 ) //range for all L-score tracks
{
if( isFull )
{
min0 = whichSampleNum( minRange, tg->minRange, tg->maxRange, binCount );
max0 = whichSampleNum( maxRange, tg->minRange, tg->maxRange, binCount );
for( i=1; i<=6; i++ )
drawWiggleHorizontalLine(hvg, (double)i, min0, max0,
binCount, y, hFactor, heightPer, gridColor );
}
}
for(lf = tg->items; lf != NULL; lf = lf->next)
{
gapPrevX = -1;
prevX = -1;
ybase = (int)((double)y+hFactor+(double)heightPer);
for (sf = lf->components; sf != NULL; sf = sf->next)
{
sampleX = sf->start;
sampleY = sf->end - sampleX; // Stange encoding but so it is.
// It is to deal with the fact that
// for a BED: sf->end = sf->start + length
// but in our case length = height (or y-value)
// so to recover height we take
// height = sf->end - sf->start.
// Otherwise another sf variable would
// be needed.
/*mapping or sequencing gap*/
if (sampleY == 0)
{
bin = -whichSampleBin( (int)((maxRange - minRange)/5.0+minRange),
minRange, maxRange, binCount );
y1 = (int)((double)y+((double)bin)* hFactor+(double)heightPer);
if( gapPrevX >= 0 )
drawScaledBox(hvg, sampleX, gapPrevX, scale,
xOff, (int)y1, (int)(.10*heightPer), shadesOfGray[2]);
gapPrevX = sampleX;
prevX = -1; /*connect next point with gray bar too*/
continue;
}
if (sampleY > maxRange)
sampleY = maxRange;
if (sampleY < minRange)
sampleY = minRange;
bin = -whichSampleBin( sampleY, minRange, maxRange, binCount );
x1 = round((double)(sampleX-winStart)*scale) + xOff;
y1 = (int)((double)y+((double)bin)* hFactor+(double)heightPer);
if (prevX > 0)
{
y2 = prevY;
x2 = round((double)(prevX-winStart)*scale) + xOff;
if( wiggleType == wiggleLinearInterpolation )
/*connect samples*/
{
if( lineGapSize < 0 || prevX - sampleX <= lineGapSize )
/*don't interpolate over large gaps*/
{
if (fill)
hvGfxFillUnder(hvg, x1,y1, x2,y2, ybase, bColor);
else
hvGfxLine(hvg, x1,y1, x2,y2, color);
}
}
}
//if( x1 < 0 || x1 > tl.picWidth )
//printf("x1 = %d, sampleX=%d, winStart = %d\n<br>", x1, sampleX, winStart );
if( x1 >= 0 && x1 <= tl.picWidth )
{
/* Draw the points themselves*/
drawScaledBox(hvg, sampleX, sampleX+1, scale, xOff, (int)y1-1, 3, color);
if( fill )
drawScaledBox(hvg, sampleX, sampleX+1, scale, xOff, (int)y1+2,
ybase-y1-2, bColor);
}
prevX = gapPrevX = sampleX;
prevY = y1;
}
leftSide = max( tg->itemStart(tg,lf), winStart );
rightSide = min( tg->itemEnd(tg,lf), winEnd );
currentX = round((double)((int)leftSide-winStart)*scale) + xOff;
currentXEnd = round((double)((int)rightSide-winStart)*scale) + xOff;
currentWidth = currentXEnd - currentX;
if( noZoom && isFull )
{
fprintf(stderr, "mapBoxHc(id: %s;) in wiggleLinkedFeatures\n",
tg->track);
mapBoxHc(hvg, lf->start, lf->end, currentX ,y, currentWidth,
heightPer, tg->track, tg->mapItemName(tg, lf), tg->itemName(tg, lf));
if( lf->next != NULL )
y += sampleUpdateY( lf->name, lf->next->name, lineHeight );
else
y += lineHeight;
}
}
}
