void mapZoomIn(int x, int y, int width, int height, double zx, double zy, double zScale)
/* Print out image map rectangle that calls self with zoom info. */
{
printf("<AREA SHAPE=RECT COORDS=\"%d,%d,%d,%d\" ", x, y, x+width, y+height);
printf("HREF=\"../cgi-bin/wikiPlot?contigDir=%s&mapX=%s&mapY=%s&pix=%d&xOff=%f&yOff=%f&zoom=%f\" ",
cgiEncode(contigDir), cgiEncode(mapX), cgiEncode(mapY), pix, zx, zy, zScale);
printf(">\n");
}
static char *encodedHgSessionReturnUrl(char *hgsid)
/* Return a CGI-encoded hgSession URL with hgsid. Free when done. */
{
char retBuf[1024];
safef(retBuf, sizeof(retBuf), "http%s://%s/cgi-bin/hgSession?hgsid=%s",
cgiAppendSForHttps(), cgiServerNamePort(), hgsid);
return cgiEncode(retBuf);
}
static char *encodedHgSessionReturnUrl(int hgsid)
/* Return a CGI-encoded hgSession URL with hgsid. Free when done. */
{
char retBuf[1024];
safef(retBuf, sizeof(retBuf), "http://%s/cgi-bin/hgSession?hgsid=%d",
cgiServerName(), hgsid);
return cgiEncode(retBuf);
}
char *insertUserPasswordIntoUrl(char *url, char *user, char *password)
/* Insert cgi-encoded user and password into url after protocol. Free returned string when done. */
{
char resultUrl[1024];
char *encUser = cgiEncode(user);
char *encPassword = cgiEncode(password);
char *rest = stringIn("://", url);
if (!rest)
errAbort("expected url [%s] to have ://", url);
char *protocol = cloneStringZ(url, rest - url);
rest += strlen("://");
safef(resultUrl, sizeof resultUrl, "%s://%s:%s@%s", protocol, encUser, encPassword, rest);
freeMem(protocol);
freeMem(encUser);
freeMem(encPassword);
return cloneString(resultUrl);
}
static void appendCgiVar(struct dyString *dy, char *name, char *value)
/* Append cgiVar with cgi-encoded value to dy. */
{
char *enc = NULL;
if (value == NULL)
value = "";
enc = cgiEncode(value);
if (dy->stringSize != 0)
dyStringAppendC(dy, '&');
dyStringAppend(dy, name);
dyStringAppendC(dy, '=');
dyStringAppend(dy, enc);
freez(&enc);
}
char *gsUploadUrl(char *gsToken, char *user, char *uploadFileName, off_t contentLength, char *base64Md5, char *contentType)
/* call uploadurl */
{
// UPLOADURLS
// TODO deal with creating parent dirs if uploadFileName contains a path? maybe not.
// old: "https://identity.genomespace.org/datamanager/uploadurls/users/"
// old "https://dm.genomespace.org/datamanager/v1.0/uploadurl/users/" // if this works, use default dir fetched earlier instead
char *dmSvr = getGenomeSpaceConfig("dmServer");
char uploadUrl[1024];
safef(uploadUrl, sizeof(uploadUrl),
"%s/v1.0/uploadurl/users/"
"%s/"
"%s"
"?Content-Length=%lld"
"&Content-MD5=%s"
"&Content-Type=%s"
, dmSvr
, user
, uploadFileName
, (long long) contentLength
, cgiEncode(base64Md5)
, contentType
);
struct dyString *reqExtra = newDyString(256);
dyStringPrintf(reqExtra, "Cookie: gs-token=%s\r\n", gsToken);
int sd = netOpenHttpExt(uploadUrl, "GET", reqExtra->string);
if (sd < 0)
errAbort("failed to open socket for [%s]", uploadUrl);
char *responseCode = NULL;
char *s3UploadUrl = parseResponse(sd, &responseCode);
if (sameString(responseCode, "404 Not Found"))
errAbort("GenomeSpace: %s, if a path was used in the output name, it may indicate the path does not exist in GenomeSpace.", responseCode);
if (!sameString(responseCode, "200 OK"))
errAbort("GenomeSpace: %s", responseCode);
dyStringFree(&reqExtra);
return s3UploadUrl;
}
static void gadPrint(struct section *section,
struct sqlConnection *conn, char *geneId)
/* Print out GAD section. */
{
int refPrinted = 0;
boolean showCompleteGadList;
char condStr[256];
char query[256];
struct sqlResult *sr;
char **row;
struct dyString *currentCgiUrl;
char *upperDisease;
char *url =
cloneString("http://geneticassociationdb.nih.gov/cgi-bin/tableview.cgi?table=allview&cond=gene=");
char *itemName;
if (url != NULL && url[0] != 0)
{
safef(condStr, sizeof(condStr),
"k.kgId='%s' and k.geneSymbol = g.geneSymbol", geneId);
itemName = sqlGetField(database, "kgXref k, gadAll g", "k.geneSymbol", condStr);
showCompleteGadList = FALSE;
if (cgiOptionalString("showAllRef") != NULL)
{
if (sameWord(cgiOptionalString("showAllRef"), "Y") ||
sameWord(cgiOptionalString("showAllRef"), "y") )
{
showCompleteGadList = TRUE;
}
}
currentCgiUrl = cgiUrlString();
printf("<B>Genetic Association Database: ");
printf("<A HREF=\"%s'%s'\" target=_blank>", url, itemName);
printf("%s</B></A>\n", itemName);
printf("<BR><B>CDC HuGE Published Literature: ");
printf("<A HREF=\"%s%s%s\" target=_blank>",
"http://hugenavigator.net/HuGENavigator/searchSummary.do?firstQuery=",
itemName,
"&publitSearchType=now&whichContinue=firststart&check=n&dbType=publit&Mysubmit=go");
printf("%s</B></A>\n", itemName);
/* List diseases associated with the gene */
safef(query, sizeof(query),
"select distinct broadPhen from gadAll where geneSymbol='%s' and association = 'Y' order by broadPhen",
itemName);
sr = sqlMustGetResult(conn, query);
row = sqlNextRow(sr);
if (row != NULL)
{
upperDisease = replaceChars(row[0], "'", "''");
touppers(upperDisease);
printf("<BR><B>Positive Disease Associations: </B>");
printf("<A HREF=\"%s%s%s%s%s\" target=_blank>",
"http://geneticassociationdb.nih.gov/cgi-bin/tableview.cgi?table=allview&cond=upper(DISEASE)%20like%20'%25",
cgiEncode(upperDisease), "%25'%20AND%20upper(GENE)%20%20like%20'%25", itemName, "%25'");
printf("%s</B></A>\n", row[0]);
row = sqlNextRow(sr);
}
while (row != NULL)
{
upperDisease = replaceChars(row[0], "'", "''");
touppers(upperDisease);
printf(", <A HREF=\"%s%s%s%s%s\" target=_blank>",
"http://geneticassociationdb.nih.gov/cgi-bin/tableview.cgi?table=allview&cond=upper(DISEASE)%20like%20'%25",
cgiEncode(upperDisease), "%25'%20AND%20upper(GENE)%20%20like%20'%25", itemName, "%25'");
printf("%s</B></A>\n", row[0]);
row = sqlNextRow(sr);
}
sqlFreeResult(&sr);
refPrinted = 0;
safef(query, sizeof(query),
"select broadPhen,reference,title,journal, pubMed, conclusion from gadAll where geneSymbol='%s' and association = 'Y' order by broadPhen",
itemName);
sr = sqlMustGetResult(conn, query);
row = sqlNextRow(sr);
if (row != NULL) printf("<BR><B>Related Studies: </B><OL>");
while (row != NULL)
{
printf("<LI><B>%s </B>", row[0]);
printf("<br>%s, %s, %s.\n", row[1], row[2], row[3]);
if (!sameWord(row[4], ""))
{
printf(" [PubMed ");
printf("<A HREF=\"%s%s%s'\" target=_blank>",
"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=Abstract&list_uids=",
row[4],"&query_hl=1&itool=genome.ucsc.edu");
printf("%s</B></A>]\n", row[4]);
}
printf("<br><i>%s</i>\n", row[5]);
printf("</LI>\n");
refPrinted++;
if ((!showCompleteGadList) && (refPrinted >= 3)) break;
row = sqlNextRow(sr);
}
sqlFreeResult(&sr);
printf("</OL>");
if ((!showCompleteGadList) && (row != NULL))
{
printf("<B>   more ... </B>");
printf(
"<A HREF=\"%s?showAllRef=Y&%s#gad\">click here to view the complete list</A> ",
"hgGene", currentCgiUrl->string);
}
}
}
static void cgDrawEither(struct track *tg, int seqStart, int seqEnd,
struct hvGfx *hvg, int xOff, int yOff, int width,
MgFont *font, Color color, enum trackVisibility vis,
char *binFileName)
/* Draw chromosome graph - either built in or not. */
{
struct chromGraphSettings *cgs = tg->customPt;
int x,y,lastX=0,lastY=0, llastX = 0, llastY = 0;
int height = tg->height;
int maxGapToFill = cgs->maxGapToFill;
int lastPos = -maxGapToFill-1;
double minVal = cgs->minVal;
double yScale = (height-1)/(cgs->maxVal - minVal);
double xScale = scaleForPixels(width);
Color myColor = cgColorLikeHgGenome(tg, hvg);
/* Draw background lines in full mode. */
if (vis == tvFull && cgs->linesAtCount != 0)
{
int i;
Color lightBlue = hvGfxFindRgb(hvg, &guidelineColor);
for (i=0; i<cgs->linesAtCount; ++i)
{
y = height - 1 - (cgs->linesAt[i] - minVal)*yScale + yOff;
hvGfxBox(hvg, xOff, y, width, 1, lightBlue);
}
}
if (binFileName)
{
struct chromGraphBin *cgb = chromGraphBinOpen(binFileName);
if (chromGraphBinSeekToChrom(cgb, chromName))
{
int seqStartMinus = seqStart - cgs->maxGapToFill;
while (chromGraphBinNextVal(cgb))
{
int pos = cgb->chromStart;
if (pos >= seqStartMinus)
{
double val = cgb->val;
x = (pos - seqStart)*xScale + xOff;
y = height - 1 - (val - minVal)*yScale + yOff;
if (x >= xOff)
{
if (pos - lastPos <= maxGapToFill)
{
if (llastX != lastX || llastY != lastY || lastX != x || lastY != y)
hvGfxLine(hvg, lastX, lastY, x, y, myColor);
}
else
hvGfxDot(hvg, x, y, myColor);
}
llastX = lastX;
llastY = lastY;
lastX = x;
lastY = y;
lastPos = pos;
if (pos >= seqEnd)
break;
}
}
}
}
else
{
struct sqlConnection *conn = hAllocConn(database);
char query[512];
struct sqlResult *sr;
char **row;
/* Construct query. Set up a little more than window so that
* we can draw connecting lines. */
sqlSafef(query, sizeof(query),
"select chromStart,val from %s "
"where chrom='%s' and chromStart>=%d and chromStart<%d",
tg->table, chromName,
seqStart - cgs->maxGapToFill, seqEnd + cgs->maxGapToFill);
sr = sqlGetResult(conn, query);
/* Loop through drawing lines from one point to another unless
* the points are too far apart. */
while ((row = sqlNextRow(sr)) != NULL)
{
int pos = sqlUnsigned(row[0]);
double val = atof(row[1]);
x = (pos - seqStart)*xScale + xOff;
y = height - 1 - (val - minVal)*yScale + yOff;
if (x >= xOff)
{
if (pos - lastPos <= maxGapToFill)
{
if (llastX != lastX || llastY != lastY || lastX != x || lastY != y)
hvGfxLine(hvg, lastX, lastY, x, y, myColor);
}
else
hvGfxDot(hvg, x, y, myColor);
}
llastX = lastX;
llastY = lastY;
lastX = x;
lastY = y;
lastPos = pos;
if (pos >= seqEnd)
break;
}
sqlFreeResult(&sr);
hFreeConn(&conn);
}
/* Do map box */
xOff = hvGfxAdjXW(hvg, xOff, width);
char *encodedTrack = cgiEncode(tg->track);
if (theImgBox && curImgTrack)
{
char link[512]; // FIXME: winStart/winEnd are not right when using a portal
safef(link,sizeof(link),"%s&c=%s&o=%d&t=%d&g=%s", hgcNameAndSettings(),
chromName, winStart, winEnd, encodedTrack);
#ifdef IMAGEv2_SHORT_MAPITEMS
if (xOff < insideX && xOff+width > insideX)
warn("cgDrawEither(%s) map item spanning slices. LX:%d TY:%d RX:%d BY:%d link:[%s]",
encodedTrack,xOff, yOff, xOff+width, yOff+height, link);
#endif//def IMAGEv2_SHORT_MAPITEMS
imgTrackAddMapItem(curImgTrack,link,NULL,xOff,yOff,xOff+width,yOff+height,tg->track);
}
else
{
hPrintf("<AREA SHAPE=RECT COORDS=\"%d,%d,%d,%d\" ", xOff, yOff, xOff+width,
yOff+height);
hPrintf("HREF=\"%s&o=%d&t=%d&g=%s&c=%s&l=%d&r=%d&db=%s&pix=%d\">\n",
hgcNameAndSettings(), winStart, winEnd, encodedTrack, chromName, winStart, winEnd,
database, tl.picWidth);
}
}
static void webStartWrapperDetailedInternal(struct cart *theCart,
char *db, char *headerText, char *textOutBuf,
boolean withHttpHeader, boolean withLogo, boolean skipSectionHeader,
boolean withHtmlHeader)
/* output a CGI and HTML header with the given title in printf format */
{
char uiState[256];
char *scriptName = cgiScriptName();
boolean isEncode = FALSE;
if (theCart)
{
char *theGenome = NULL;
char *genomeEnc = NULL;
getDbAndGenome(theCart, &db, &theGenome, NULL);
genomeEnc = cgiEncode(theGenome);
safef(uiState, sizeof(uiState), "?%s=%s&%s=%s&%s=%u",
orgCgiName, genomeEnc,
dbCgiName, db,
cartSessionVarName(), cartSessionId(theCart));
}
else
{
uiState[0] = 0;
uiState[1] = 0;
}
if (db == NULL)
db = hDefaultDb();
boolean dbIsFound = hDbExists(db);
boolean haveBlat = FALSE;
if (dbIsFound)
haveBlat = hIsBlatIndexedDatabase(db);
if (scriptName == NULL)
scriptName = cloneString("");
/* don't output two headers */
if(webHeadAlreadyOutputed)
return;
if (sameString(cgiUsualString("action",""),"encodeReleaseLog") ||
rStringIn("EncodeDataVersions", scriptName))
isEncode = TRUE;
/* Preamble. */
dnaUtilOpen();
if (withHttpHeader)
puts("Content-type:text/html\n");
if (withHtmlHeader)
{
char *newString, *ptr1, *ptr2;
char *browserVersion;
if (btIE == cgiClientBrowser(&browserVersion, NULL, NULL) && *browserVersion < '8')
puts("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 3.2//EN\">");
else
puts("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Transitional//EN\" "
"\"http://www.w3.org/TR/html4/loose.dtd\">");
// Strict would be nice since it fixes atleast one IE problem (use of :hover CSS pseudoclass)
puts(
"<HTML>" "\n"
"<HEAD>" "\n"
);
printf("\t%s\n", headerText);
printf("\t<META HTTP-EQUIV=\"Content-Type\" CONTENT=\"text/html;CHARSET=iso-8859-1\">" "\n"
"\t<META http-equiv=\"Content-Script-Type\" content=\"text/javascript\">" "\n"
"\t<META HTTP-EQUIV=\"Pragma\" CONTENT=\"no-cache\">" "\n"
"\t<META HTTP-EQUIV=\"Expires\" CONTENT=\"-1\">" "\n"
"\t<TITLE>"
);
/* we need to take any HTML formatting out of the titlebar string */
newString = cloneString(textOutBuf);
for(ptr1=newString, ptr2=textOutBuf; *ptr2 ; ptr2++)
{
if (*ptr2 == '<')
{
for(; *ptr2 && (*ptr2 != '>'); ptr2++)
;
}
else
*ptr1++ = *ptr2;
}
*ptr1 = 0;
htmlTextOut(newString);
printf(" </TITLE>\n ");
webIncludeResourceFile("HGStyle.css");
if (extraStyle != NULL)
puts(extraStyle);
printf("</HEAD>\n");
printBodyTag(stdout);
htmlWarnBoxSetup(stdout);// Sets up a warning box which can be filled with errors as they occur
puts(commonCssStyles());
}
puts(
"<A NAME=\"TOP\"></A>" "\n"
"" "\n"
"<TABLE BORDER=0 CELLPADDING=0 CELLSPACING=0 WIDTH=\"100%\">" "\n");
if (withLogo)
{
puts("<TR><TH COLSPAN=1 ALIGN=\"left\">");
if (isEncode)
{
puts("<A HREF=\"http://www.genome.gov/10005107\" TARGET=\"_BLANK\">"
"<IMG SRC=\"../images/ENCODE_scaleup_logo.png\" height=50 ALT=\"ENCODE Project at NHGRI\">"
"</A>");
puts("<IMG SRC=\"../images/encodeDcc.jpg\" ALT=\"ENCODE Project at UCSC\">");
}
else
{
puts("<IMG SRC=\"../images/title.jpg\">");
}
puts("</TH></TR>" "\n"
"" "\n" );
}
/* Put up the hot links bar. */
char *menuStr = menuBar(theCart);
if(menuStr)
{
puts(menuStr);
}
if (endsWith(scriptName, "hgGateway") && geoMirrorEnabled())
{
// Show an opt-out alert if user is on a host to which user has been automatically redirected (just once, right after they have been redirected)
char *source = cgiOptionalString("source");
char *redirect = cgiOptionalString("redirect");
if (source != NULL && redirect != NULL && sameString(redirect, "auto"))
{
char *domain = cgiServerName();
char *port = cgiServerPort();
// We don't bother maintaining stuff in request URI, because it may contain items like hgsid and other host specific values
int newUriSize = 2048;
char *newUri = needMem(newUriSize);
safef(newUri, newUriSize, "http%s://%s:%s/cgi-bin/hgGateway?redirect=manual&source=%s",
cgiServerHttpsIsOn() ? "s" : "", source, port, domain);
printf("<TR><TD COLSPAN=3 id='redirectTd' onclick=\"javascript:document.getElementById('redirectTd').innerHTML='';\">"
"<div style=\"margin: 10px 25%%; border-style:solid; border-width:thin; border-color:#97D897;\">"
"<h3 style=\"background-color: #97D897; text-align: left; margin-top:0px; margin-bottom:0px;\">"
" You've been redirected to your nearest mirror - %s"
"<idiv style=\"float:right;\">[x]</idiv>"
"</h3> "
"<ul style=\"margin:5px;\">"
"<li>Take me back to <a href=\"%s\">%s</a>"
"<idiv style=\"float:right;\"><a href=\"../goldenPath/help/genomeEuro.html\">What is this?</a></idiv>"
"</li>"
"</ul>"
"</div>"
"</TD></TR>\n"
, domain, newUri, source );
}
}
if(!skipSectionHeader)
/* this HTML must be in calling code if skipSectionHeader is TRUE */
{
puts( // TODO: Replace nested tables with CSS (difficulty is that tables are closed elsewhere)
"<!-- +++++++++++++++++++++ CONTENT TABLES +++++++++++++++++++ -->" "\n"
"<TR><TD COLSPAN=3>\n"
"<div id=firstSection>"
" <!--outer table is for border purposes-->\n"
" <TABLE WIDTH='100%' BGCOLOR='#" HG_COL_BORDER "' BORDER='0' CELLSPACING='0' "
"CELLPADDING='1'><TR><TD>\n"
" <TABLE BGCOLOR='#" HG_COL_INSIDE "' WIDTH='100%' BORDER='0' CELLSPACING='0' "
"CELLPADDING='0'><TR><TD>\n"
" <div class='subheadingBar'><div class='windowSize' id='sectTtl'>"
);
htmlTextOut(textOutBuf);
puts(" </div></div>\n"
" <TABLE BGCOLOR='#" HG_COL_INSIDE "' WIDTH='100%' CELLPADDING=0>"
"<TR><TH HEIGHT=10></TH></TR>\n"
" <TR><TD WIDTH=10> </TD><TD>\n\n"
);
};
webPushErrHandlers();
/* set the flag */
webHeadAlreadyOutputed = TRUE;
} /* static void webStartWrapperDetailedInternal() */
static struct linkedFeatures *cgapSageToLinkedFeatures(struct cgapSage *tag,
struct hash *libHash, struct hash *libTotHash, enum trackVisibility vis)
/* Convert a single CGAP tag to a list of linkedFeatures. */
{
struct linkedFeatures *libList = NULL;
struct linkedFeatures *skel = skeletonLf(tag);
int i;
if (vis == tvDense)
/* Just use the skeleton one. */
{
int tagTotal = 0;
int freqTotal = 0;
int libsUsed = 0;
for (i = 0; i < tag->numLibs; i++)
{
char libId[16];
char *libName;
safef(libId, sizeof(libId), "%d", tag->libIds[i]);
libName = hashMustFindVal(libHash, libId);
if (keepThisLib(libName, libId))
{
int libTotal = hashIntVal(libTotHash, libId);
tagTotal += libTotal;
freqTotal += tag->freqs[i];
libsUsed++;
}
}
if (libsUsed > 0)
{
skel->name = cloneString("whatever");
skel->score = (float)((double)freqTotal * (1000000/tagTotal));
skel->grayIx = grayIxForCgap(skel->score);
addSimpleFeature(skel);
libList = skel;
}
}
else if (vis == tvPack)
{
/* If it's pack mode, average tissues into one linkedFeature. */
struct hash *tpmHash = combineCgapSages(tag, libHash, libTotHash);
struct hashEl *tpmList = hashElListHash(tpmHash);
struct hashEl *tpmEl;
slSort(&tpmList, slNameCmp);
for (tpmEl = tpmList; tpmEl != NULL; tpmEl = tpmEl->next)
{
struct linkedFeatures *tiss = CloneVar(skel);
struct cgapSageTpmHashEl *tpm = (struct cgapSageTpmHashEl *)tpmEl->val;
char link[256];
char *encTissName = NULL;
double score = 0;
int len = strlen(tpmEl->name) + 32;
tiss->name = needMem(len);
safef(tiss->name, len, "%s (%d)", tpmEl->name, tpm->count);
encTissName = cgiEncode(tpmEl->name);
safef(link, sizeof(link), "i=%s&tiss=%s", tag->name, encTissName);
score = (double)tpm->freqTotal*(1000000/(double)tpm->libTotals);
tiss->score = (float)score;
tiss->grayIx = grayIxForCgap(score);
tiss->extra = cloneString(link);
freeMem(encTissName);
addSimpleFeature(tiss);
slAddHead(&libList, tiss);
}
hashElFreeList(&tpmList);
freeHashAndVals(&tpmHash);
}
else
/* full mode */
{
for (i = 0; i < tag->numLibs; i++)
{
char libId[16];
char *libName;
char link[256];
struct linkedFeatures *lf;
safef(libId, sizeof(libId), "%d", tag->libIds[i]);
libName = hashMustFindVal(libHash, libId);
if (keepThisLib(libName, libId))
{
lf = CloneVar(skel);
lf->name = cloneString(libName);
safef(link, sizeof(link), "i=%s&lib=%s", tag->name, libId);
lf->score = (float)tag->tagTpms[i];
lf->grayIx = grayIxForCgap(tag->tagTpms[i]);
lf->extra = cloneString(link);
addSimpleFeature(lf);
slAddHead(&libList, lf);
}
}
}
slSort(&libList, cgapLinkedFeaturesCmp);
slReverse(&libList);
return libList;
}
static void hgPositionsJson(struct jsonWrite *jw, char *db, struct hgPositions *hgp, struct cart *cart)
/* Write out JSON description of multiple position matches. */
{
struct hgPosTable *table;
jsonWriteListStart(jw, "positionMatches");
struct trackDb *tdbList = NULL;
for (table = hgp->tableList; table != NULL; table = table->next)
{
if (table->posList != NULL)
{
char *tableName = table->name;
// clear the tdb cache if this track is a hub track
if (isHubTrack(tableName))
tdbList = NULL;
struct trackDb *tdb = tdbForTrack(db, tableName, &tdbList);
if (!tdb && startsWith("all_", tableName))
tdb = tdbForTrack(db, tableName+strlen("all_"), &tdbList);
if (!tdb)
errAbort("no track for table \"%s\" found via a findSpec", tableName);
char *trackName = tdb->track;
jsonWriteObjectStart(jw, NULL);
jsonWriteString(jw, "name", table->name);
jsonWriteString(jw, "trackName", trackName);
jsonWriteString(jw, "description", table->description);
jsonWriteString(jw, "vis", hCarefulTrackOpenVis(db, trackName));
jsonWriteListStart(jw, "matches");
struct hgPos *pos;
for (pos = table->posList; pos != NULL; pos = pos->next)
{
char *encMatches = cgiEncode(pos->browserName);
jsonWriteObjectStart(jw, NULL); // begin one match
if (pos->chrom != NULL)
jsonWriteStringf(jw, "position", "%s:%d-%d",
pos->chrom, pos->chromStart+1, pos->chromEnd);
else
// GenBank results set position to GB accession instead of chr:s-e position.
jsonWriteString(jw, "position", pos->name);
// this is magic to tell the browser to make the
// composite and this subTrack visible
if (tdb->parent)
{
if (tdbIsSuperTrackChild(tdb))
jsonWriteStringf(jw, "extraSel", "%s=show&", tdb->parent->track);
else
{
// tdb is a subtrack of a composite or a view
jsonWriteStringf(jw, "extraSel", "%s_sel=1&%s_sel=1&",
trackName, tdb->parent->track);
}
}
jsonWriteString(jw, "hgFindMatches", encMatches);
jsonWriteString(jw, "posName", htmlEncodeText(pos->name, FALSE));
if (pos->description)
{
stripString(pos->description, "\n");
jsonWriteString(jw, "description", stripAnchor(pos->description));
}
jsonWriteObjectEnd(jw); // end one match
}
jsonWriteListEnd(jw); // end matches
jsonWriteObjectEnd(jw); // end one table
}
}
jsonWriteListEnd(jw); // end positionMatches
}
void mafPrettyOut(FILE *f, struct mafAli *maf, int lineSize,
boolean onlyDiff, int blockNo)
{
int ii, ch;
int srcChars = 0;
struct mafComp *mc;
int lineStart, lineEnd;
char *summaryLine = needMem(lineSize+1);
char *referenceText;
int startChars, sizeChars, srcSizeChars;
boolean haveInserts = FALSE;
struct mafComp *masterMc = maf->components;
startChars = sizeChars = srcSizeChars = 0;
for (mc = maf->components; mc != NULL; mc = mc->next)
{
/* Figure out length of source (species) field. */
/*if (mc->size != 0)*/
{
char dbOnly[128];
int len;
char *org;
memset(dbOnly, 0, sizeof(dbOnly));
safef(dbOnly, sizeof(dbOnly), "%s", mc->src);
chopPrefix(dbOnly);
if ((org = hOrganism(dbOnly)) == NULL)
len = strlen(dbOnly);
else
len = strlen(org);
if (srcChars < len)
srcChars = len;
len = digitsBaseTen(mc->start);
if (startChars < len)
startChars = len;
len = digitsBaseTen(mc->size);
if (sizeChars < len)
sizeChars = len;
len = digitsBaseTen(mc->srcSize);
if (srcSizeChars < len)
srcSizeChars = len;
if (mc->text && (mc->rightStatus == MAF_INSERT_STATUS) && (masterMc->start + masterMc->size < winEnd))
haveInserts = TRUE;
#ifdef REVERSESTRAND
/* complement bases if hgTracks is on reverse strand */
if (mc->size && cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE))
complement(mc->text, maf->textSize);
#endif
}
}
/* first sequence in the alignment */
referenceText = maf->components->text;
for (lineStart = 0; lineStart < maf->textSize; lineStart = lineEnd)
{
int size;
lineEnd = lineStart + lineSize;
if (lineEnd >= maf->textSize)
lineEnd = maf->textSize;
size = lineEnd - lineStart;
initSummaryLine(summaryLine, size, '*');
for (mc = maf->components; mc != NULL; mc = mc->next)
{
char dbOnly[128], *chrom;
int s = mc->start;
int e = s + mc->size;
char *org;
char *revComp = "";
char strand = mc->strand;
struct dyString *dy = newDyString(512);
#ifdef REVERSESTRAND
if (cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE))
strand = (strand == '+') ? '-' : '+';
#endif
if (strand == '-') revComp = "&hgSeq.revComp=on";
dyStringClear(dy);
safef(dbOnly, sizeof(dbOnly), "%s", mc->src);
chrom = chopPrefix(dbOnly);
if ((org = hOrganism(dbOnly)) == NULL)
org = dbOnly;
if (mc->strand == '-')
reverseIntRange(&s, &e, mc->srcSize);
if (mc->text != NULL)
{
if (lineStart == 0)
{
if (hDbIsActive(dbOnly))
{
dyStringPrintf(dy, "%s Browser %s:%d-%d %c %*dbps",hOrganism(dbOnly),chrom, s+1, e, mc->strand,sizeChars, mc->size);
linkToOtherBrowserTitle(dbOnly, chrom, s, e, dy->string);
dyStringClear(dy);
fprintf(f, "B</A> ");
}
else
fprintf(f, " ");
if (hDbExists(dbOnly))
{
dyStringPrintf(dy, "Get %s DNA %s:%d-%d %c %*dbps",hOrganism(dbOnly),chrom, s+1, e, mc->strand,sizeChars, mc->size);
printf("<A TITLE=\"%s\" TARGET=\"_blank\" HREF=\"%s?o=%d&g=getDna&i=%s&c=%s&l=%d&r=%d&db=%s%s\">D</A> ", dy->string,hgcName(),
s, cgiEncode(chrom),
chrom, s, e, dbOnly, revComp);
}
else
fprintf(f, " ");
}
else
{
fprintf(f, " ");
}
dyStringClear(dy);
dyStringPrintf(dy, "%s:%d-%d %c %*dbps",chrom, s+1, e, mc->strand,sizeChars, mc->size);
fprintf(f, "<A TITLE=\"%s\"> %*s </A> ", dy->string, srcChars, org);
updateSummaryLine(summaryLine, referenceText + lineStart, mc->text + lineStart, size);
blueCapWrite(f, mc->text + lineStart, size,
(onlyDiff && mc != maf->components) ? referenceText + lineStart : NULL);
fprintf(f, "\n");
}
else
{
if (((mc->leftStatus == MAF_CONTIG_STATUS) && (mc->rightStatus == MAF_CONTIG_STATUS) )
|| ((mc->leftStatus == MAF_TANDEM_STATUS) && (mc->rightStatus == MAF_TANDEM_STATUS) )
|| ((mc->leftStatus == MAF_INSERT_STATUS) && (mc->rightStatus == MAF_INSERT_STATUS) )
|| ((mc->leftStatus == MAF_MISSING_STATUS) && (mc->rightStatus == MAF_MISSING_STATUS) ))
{
if (lineStart == 0)
{
int s = mc->start;
int e = s + mc->rightLen;
struct dyString *dy = newDyString(512);
if (mc->strand == '-')
reverseIntRange(&s, &e, mc->srcSize);
if ( hDbIsActive(dbOnly))
{
dyStringPrintf(dy, "%s Browser %s:%d-%d %c %d bps Unaligned",hOrganism(dbOnly),chrom, s+1, e, mc->strand, e-s);
linkToOtherBrowserTitle(dbOnly, chrom, s, e, dy->string);
fprintf(f,"B</A> ");
dyStringClear(dy);
}
else
fprintf(f," ");
if (hDbExists(dbOnly))
{
dyStringPrintf(dy, "Get %s DNA %s:%d-%d %c %d bps Unaligned",hOrganism(dbOnly),chrom, s+1, e, mc->strand, e-s);
printf("<A TITLE=\"%s\" TARGET=\"_blank\" HREF=\"%s?o=%d&g=getDna&i=%s&c=%s&l=%d&r=%d&db=%s%s\">D</A> ", dy->string, hgcName(),
s, cgiEncode(chrom),
chrom, s, e, dbOnly,revComp);
}
else
fprintf(f, " ");
}
else
fprintf(f, " ");
initSummaryLine(summaryLine, size, ' ');
dyStringClear(dy);
dyStringPrintf(dy, "%s:%d-%d %c %*dbps",chrom, s+1, e, mc->strand,sizeChars, mc->size);
fprintf(f, "<A TITLE=\"%s\">%*s</A> ", dy->string, srcChars, org);
ch = '-';
switch(mc->rightStatus)
{
case MAF_INSERT_STATUS:
ch = '=';
break;
case MAF_MISSING_STATUS:
ch = 'N';
break;
case MAF_TANDEM_STATUS:
case MAF_CONTIG_STATUS:
ch = '-';
break;
}
for(ii=lineStart; ii < lineEnd ; ii++)
fputc(ch,f);
fprintf(f,"\n");
}
}
}
#ifdef ADDMATCHLINE
if (lineStart == 0)
fprintf(f, " %-*s %s\n", srcChars, "", summaryLine);
else
fprintf(f, "%-*s %s\n", srcChars, "", summaryLine);
#else
fprintf(f, "\n");
#endif
}
if (haveInserts)
{
fprintf(f, "<B>Inserts between block %d and %d in window</B>\n",blockNo, blockNo+1);
for (mc = maf->components; mc != NULL; mc = mc->next)
{
char dbOnly[128], *chrom;
int s = mc->start + mc->size;
int e = s + mc->rightLen;
char *org;
if (mc->text == NULL)
continue;
if (mc->strand == '-')
reverseIntRange(&s, &e, mc->srcSize);
safef(dbOnly, sizeof(dbOnly), "%s", mc->src);
chrom = chopPrefix(dbOnly);
if ((org = hOrganism(dbOnly)) == NULL)
org = dbOnly;
if (mc->rightStatus == MAF_INSERT_STATUS)
{
char *revComp = "";
if (hDbIsActive(dbOnly))
{
char strand = mc->strand;
#ifdef REVERSESTRAND
if (cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE))
strand = (strand == '+') ? '-' : '+';
#endif
if (strand == '-') revComp = "&hgSeq.revComp=on";
linkToOtherBrowser(dbOnly, chrom, s, e);
fprintf(f,"B");
fprintf(f, "</A>");
fprintf(f, " ");
}
else
fprintf(f, " ");
if (hDbExists(dbOnly))
{
printf("<A TARGET=\"_blank\" HREF=\"%s?o=%d&g=getDna&i=%s&c=%s&l=%d&r=%d"
"&db=%s%s\">D</A> ", hgcName(), s, cgiEncode(chrom), chrom, s,
e, dbOnly,revComp);
}
else
fprintf(f, " ");
fprintf(f, "%*s %dbp\n", srcChars, org,mc->rightLen);
}
}
fprintf(f, "\n");
}
freeMem(summaryLine);
}
void presentProteinSelections(char *queryID, int protCntInSwissByGene, int protCntInSupportedGenomeDb)
/* Fuction to present a web page with proteins of different organisms */
{
char *gDatabase;
char *org = NULL;
char *spID, *displayID, *desc;
char cond_str[255];
struct sqlConnection *conn, *conn3;
char query[256], query3[512];
struct sqlResult *sr, *sr3;
char **row, **row3;
struct sqlConnection *connCentral, *proteinsConn;
char queryCentral[256];
struct sqlResult *srCentral;
char *answer;
char *taxonId, *protAcc, *protDisp, *protOrg, *protDesc;
char *oldOrg, *orgSciName;
char *pbOrgSciName[MAX_PB_ORG];
boolean pbOrgPresented[MAX_PB_ORG];
boolean skipIt;
int i, maxPbOrg;
int otherCnt;
connCentral = hConnectCentral();
hPrintf("<TABLE WIDTH=\"100%%\" BGCOLOR=\"#"HG_COL_HOTLINKS"\" BORDER=\"0\" CELLSPACING=\"0\"");
hPrintf("CELLPADDING=\"2\"><TR>\n");
hPrintf("<TD ALIGN=LEFT><A HREF=\"../index.html\">%s</A></TD>", wrapWhiteFont("Home"));
hPrintf("<TD style='text-align:center; color:#FFFFFF; font-size:medium;'>%s</TD>",
"UCSC Proteome Browser");
if (proteinInSupportedGenome)
{
hPrintf("<TD ALIGN=Right><A HREF=\"../goldenPath/help/pbTracksHelpFiles/pbTracksHelp.shtml\"");
}
else
{
hPrintf("<TD ALIGN=Right><A HREF=\"../goldenPath/help/pbTracksHelpFiles/pbTracksHelp.shtml\"");
}
hPrintf("TARGET=_blank>%s</A></TD>", wrapWhiteFont("Help"));
hPrintf("</TR></TABLE>");
hPrintf("<FONT SIZE=4><BR><B>Please select one of the following proteins:<BR><BR></B></FONT>\n");
/* remmember a list of scientific names for the genomes that supports PB */
sqlSafef(queryCentral, sizeof(queryCentral),
"select distinct dbDb.scientificName from dbDb where hgPbOk=1");
srCentral = sqlMustGetResult(connCentral, queryCentral);
row3 = sqlNextRow(srCentral);
i=0;
while (row3 != NULL)
{
pbOrgSciName[i] = strdup(row3[0]);
pbOrgPresented[i] = FALSE;
i++;
row3 = sqlNextRow(srCentral);
}
maxPbOrg = i;
/* go through each genome DB that supports PB */
sqlSafef(queryCentral, sizeof(queryCentral),
"select defaultDb.name, dbDb.organism, dbDb.scientificName from dbDb,defaultDb where hgPbOk=1 and defaultDb.name=dbDb.name");
srCentral = sqlMustGetResult(connCentral, queryCentral);
row3 = sqlNextRow(srCentral);
while (row3 != NULL)
{
gDatabase = row3[0];
org = row3[1];
orgSciName= row3[2];
protDbName = hPdbFromGdb(gDatabase);
proteinsConn = sqlConnect(protDbName);
conn = sqlConnect(gDatabase);
sqlSafefFrag(cond_str, sizeof(cond_str), "alias='%s' and spID != ''", queryID);
answer = sqlGetField(gDatabase, "kgSpAlias", "count(distinct spID)", cond_str);
if ((answer != NULL) && (!sameWord(answer, "0")))
{
/* display organism name */
hPrintf("<FONT SIZE=4><B>");
hPrintf("<A href=\"http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&name=%s&lvl=0&srchmode=1\" TARGET=_blank>%s</A>",
cgiEncode(orgSciName), orgSciName);
hPrintf(" (%s):</B></FONT>\n", org);
hPrintf("<UL>");
sqlSafef(query, sizeof(query),
"select distinct spID from %s.kgSpAlias where alias='%s' "
"and spID != ''",
gDatabase, queryID);
sr = sqlMustGetResult(conn, query);
row = sqlNextRow(sr);
while (row != NULL)
{
spID = row[0];
sqlSafefFrag(cond_str, sizeof(cond_str), "accession='%s'", spID);
displayID = sqlGetField(protDbName, "spXref3", "displayID", cond_str);
sqlSafefFrag(cond_str, sizeof(cond_str), "accession='%s'", spID);
desc = sqlGetField(protDbName, "spXref3", "description", cond_str);
/* display a protein */
hPrintf(
"<LI><A HREF=\"../cgi-bin/pbGlobal?proteinID=%s&db=%s\">",
displayID, gDatabase);
if (sameWord(spID, displayID) || (strstr(displayID, spID) != NULL))
{
hPrintf("%s</A> %s\n", spID, desc);
}
else
{
hPrintf("%s</A> (aka %s) %s\n", spID, displayID, desc);
}
/* remember the fact that a protein is shown under this PB supported genome */
for (i=0; i<maxPbOrg; i++)
{
if (sameWord(orgSciName, pbOrgSciName[i]))
{
pbOrgPresented[i] = TRUE;
}
}
row = sqlNextRow(sr);
}
hPrintf("</UL>");fflush(stdout);
sqlFreeResult(&sr);
}
sqlDisconnect(&proteinsConn);
row3 = sqlNextRow(srCentral);
}
sqlFreeResult(&srCentral);
hDisconnectCentral(&connCentral);
sqlDisconnect(&conn);
if (protCntInSwissByGene > protCntInSupportedGenomeDb)
{
otherCnt = -1;
if (protCntInSupportedGenomeDb >0)
{
otherCnt = 0;
hPrintf("<FONT SIZE=4><B>Other Organisms:</B></FONT>\n");
hPrintf("<UL>");
}
else
{
hPrintf("<UL>");
}
oldOrg = strdup("");
conn3 = sqlConnect(UNIPROT_DB_NAME);
sqlSafef(query3, sizeof(query3),
"select taxon.id, gene.acc, displayId.val, binomial, description.val "
"from gene, displayId, accToTaxon,taxon, description "
"where gene.val='%s' and gene.acc=displayId.acc and accToTaxon.taxon=taxon.id "
"and accToTaxon.acc=gene.acc and description.acc=gene.acc order by binomial",
queryID);
sr3 = sqlMustGetResult(conn3, query3);
row3 = sqlNextRow(sr3);
/* go through each protein */
while (row3 != NULL)
{
taxonId = row3[0];
protAcc = row3[1];
protDisp = row3[2];
protOrg = row3[3];
protDesc = row3[4];
/* decide if this entry should be skipped */
skipIt = FALSE;
for (i=0; i<maxPbOrg; i++)
{
if (sameWord(pbOrgSciName[i], protOrg) && pbOrgPresented[i])
{
skipIt = TRUE;
}
}
/* print organism name if organism changed */
if (!sameWord(protOrg, oldOrg))
{
if (!sameWord(oldOrg, ""))
{
hPrintf("</UL>\n");
}
if (!skipIt)
{
sqlSafefFrag(cond_str, sizeof(cond_str), "id=%s and nameType='genbank common name'", taxonId);
answer = sqlGetField(PROTEOME_DB_NAME, "taxonNames", "name", cond_str);
hPrintf("<FONT SIZE=3><B>");
hPrintf("<A href=\"http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&name=%s&lvl=0&srchmode=1\" TARGET=_blank>%s</A>",
cgiEncode(protOrg), protOrg);
if (answer != NULL)
{
hPrintf(" (%s)", answer);
}
hPrintf(":</B></FONT>\n");
}
hPrintf("<UL>\n");
}
/* print protein entry, if it is not already displayed in the PB supported genome list */
if (!skipIt)
{
otherCnt++;
if (sameWord(protAcc, protDisp))
{
hPrintf("<LI><A HREF=\"../cgi-bin/pbGlobal?proteinID=%s\">", protAcc);
hPrintf("%s</A> %s\n", protAcc, protDesc);
}
else
{
hPrintf("<LI><A HREF=\"../cgi-bin/pbGlobal?proteinID=%s\">", protAcc);
if (strstr(protDisp, protAcc) != NULL)
{
hPrintf("%s</A> %s\n", protAcc, protDesc);
}
else
{
hPrintf("%s</A> (aka %s) %s\n", protAcc, protDisp, protDesc);
}
}
}
oldOrg = strdup(protOrg);
row3 = sqlNextRow(sr3);
}
if (otherCnt == 0) hPrintf("</UL>None");fflush(stdout);
sqlFreeResult(&sr3);
sqlDisconnect(&conn3);
}
}
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 showAliPlaces(char *pslName, char *faName, char *database,
enum gfType qType, enum gfType tType,
char *organism, boolean feelingLucky)
/* Show all the places that align. */
{
struct lineFile *lf = pslFileOpen(pslName);
struct psl *pslList = NULL, *psl;
char *browserUrl = hgTracksName();
char *hgcUrl = hgcName();
char uiState[64];
char *vis;
char unhideTrack[64];
char *sort = cartUsualString(cart, "sort", sortList[0]);
char *output = cartUsualString(cart, "output", outputList[0]);
boolean pslOut = startsWith("psl", output);
boolean isStraightNuc = (qType == gftRna || qType == gftDna);
int minThreshold = (isStraightNuc ? minMatchShown : 0);
sprintf(uiState, "%s=%s", cartSessionVarName(), cartSessionId(cart));
/* If user has hidden BLAT track, add a setting that will unhide the
track if user clicks on a browser link. */
vis = cartOptionalString(cart, "hgUserPsl");
if (vis != NULL && sameString(vis, "hide"))
snprintf(unhideTrack, sizeof(unhideTrack), "&hgUserPsl=dense");
else
unhideTrack[0] = 0;
while ((psl = pslNext(lf)) != NULL)
{
if (psl->match >= minThreshold)
slAddHead(&pslList, psl);
}
lineFileClose(&lf);
if (pslList == NULL)
{
puts("<table><tr><td><hr>Sorry, no matches found<hr><td></tr></table>");
return;
}
if (sameString(sort, "query,start"))
{
slSort(&pslList, pslCmpQuery);
}
else if (sameString(sort, "query,score"))
{
slSort(&pslList, pslCmpQueryScore);
}
else if (sameString(sort, "score"))
{
slSort(&pslList, pslCmpScore);
}
else if (sameString(sort, "chrom,start"))
{
slSort(&pslList, pslCmpTargetStart);
}
else if (sameString(sort, "chrom,score"))
{
slSort(&pslList, pslCmpTargetScore);
}
else
{
slSort(&pslList, pslCmpQueryScore);
}
if(feelingLucky)
{
/* If we found something jump browser to there. */
if(slCount(pslList) > 0)
printLuckyRedirect(browserUrl, pslList, database, pslName, faName, uiState, unhideTrack);
/* Otherwise call ourselves again not feeling lucky to print empty
results. */
else
{
cartWebStart(cart, database, "%s BLAT Results", trackHubSkipHubName(organism));
showAliPlaces(pslName, faName, database, qType, tType, organism, FALSE);
cartWebEnd();
}
}
else if (pslOut)
{
printf("<TT><PRE>");
if (!sameString(output, "psl no header"))
pslxWriteHead(stdout, qType, tType);
for (psl = pslList; psl != NULL; psl = psl->next)
pslTabOut(psl, stdout);
printf("</PRE></TT>");
}
else
{
printf("<H2>BLAT Search Results</H2>");
printf("<TT><PRE>");
printf(" ACTIONS QUERY SCORE START END QSIZE IDENTITY CHRO STRAND START END SPAN\n");
printf("---------------------------------------------------------------------------------------------------\n");
for (psl = pslList; psl != NULL; psl = psl->next)
{
printf("<A HREF=\"%s?position=%s:%d-%d&db=%s&ss=%s+%s&%s%s\">",
browserUrl, psl->tName, psl->tStart + 1, psl->tEnd, database,
pslName, faName, uiState, unhideTrack);
printf("browser</A> ");
printf("<A HREF=\"%s?o=%d&g=htcUserAli&i=%s+%s+%s&c=%s&l=%d&r=%d&db=%s&%s\">",
hgcUrl, psl->tStart, pslName, cgiEncode(faName), psl->qName, psl->tName,
psl->tStart, psl->tEnd, database, uiState);
printf("details</A> ");
printf("%-14s %5d %5d %5d %5d %5.1f%% %4s %2s %9d %9d %6d\n",
psl->qName, pslScore(psl), psl->qStart+1, psl->qEnd, psl->qSize,
100.0 - pslCalcMilliBad(psl, TRUE) * 0.1,
skipChr(psl->tName), psl->strand, psl->tStart+1, psl->tEnd,
psl->tEnd - psl->tStart);
}
printf("</PRE></TT>");
}
pslFreeList(&pslList);
}
void configurePage()
/* Put up configuration page. */
{
cartWebStart(cart, database, "Configure Genome Graphs");
hPrintf("<FORM ACTION=\"../cgi-bin/hgGenome\" METHOD=GET>\n");
cartSaveSession(cart);
hPrintf("<TABLE>\n");
hPrintf("<TR>\n");
hPrintf("<TD>\n");
hPrintf("image width: ");
cgiMakeIntVar(hggImageWidth, cartUsualInt(cart, hggImageWidth, hgDefaultPixWidth), 4);
hPrintf("</TD>\n");
hPrintf("<TD>\n");
hPrintf("graph height: ");
cgiMakeIntVar(hggGraphHeight, graphHeight(), 3);
hPrintf("</TD>\n");
hPrintf("<TD>\n");
hPrintf(" graphs per line: ");
makeNumMenu(hggGraphsPerLine, minGraphsPerLine, maxGraphsPerLine,
graphsPerLine());
hPrintf("</TD>\n");
hPrintf("<TD>\n");
hPrintf(" lines of graphs: ");
makeNumMenu(hggLinesOfGraphs, minLinesOfGraphs, maxLinesOfGraphs,
linesOfGraphs());
hPrintf("</TD>\n");
hPrintf("</TR>\n");
hPrintf("</TABLE>\n");
hPrintf("<TABLE><TR><TD>\n");
hPrintf("chromosome layout: ");
cgiMakeDropList(hggChromLayout, chromLayouts, ArraySize(chromLayouts),
chromLayout());
hPrintf("</TD></TR></TABLE>\n");
hPrintf("<TABLE><TR><TD>\n");
hPrintf("numerical labels: ");
cartMakeCheckBox(cart, hggLabels, TRUE);
hPrintf(" <I>Label axis on left for first graph and on right for last graph</I>");
hPrintf("</TD></TR></TABLE>\n");
hPrintf("<TABLE><TR><TD>\n");
hPrintf("highlight missing: ");
cartMakeCheckBox(cart, hggYellowMissing, FALSE);
hPrintf(" <I>Highlight background in yellow/gray if there is missing data in first graph</I>");
hPrintf("</TD></TR></TABLE>\n");
hPrintf("<TABLE><TR><TD>\n");
hPrintf("region padding: ");
cgiMakeIntVar(hggRegionPad, regionPad(), 6);
hPrintf(" <I>Number of bases to add to either side of regions over threshold</I>");
hPrintf("</TD></TR></TABLE>\n");
hPrintf("<TABLE><TR><TD>\n");
cgiMakeButton("submit", "submit");
hPrintf("</TD></TR></TABLE>\n");
hPrintf("</TD>\n");
hPrintf("</FORM>\n");
webNewSection("Configure Graphs");
hPrintf("Click on the hyperlink by the graph name to configure it.");
hTableStart();
hPrintf("<TR><TH>name</TH>");
hPrintf("<TH>description</TH></TR>");
struct slRef *ref;
for (ref = ggList; ref != NULL; ref = ref->next)
{
struct genoGraph *gg = ref->val;
/* Only show custom graphs, stand-alone DB graphs, and composite */
/* graphs. Don't show subGraphs part of a composite. */
if (gg->isSubGraph == FALSE)
{
char *tmp = cgiEncode(gg->name);
hPrintf("<TR><TD><A HREF=\"../cgi-bin/hgGenome?%s&%s=on&g=%s\">",
cartSidUrlString(cart), hggConfigureOne, tmp);
freeMem(tmp);
hPrintf("%s</A></TD>", gg->shortLabel);
hPrintf("<TD>%s</TD></TR>\n", gg->longLabel);
}
}
hTableEnd();
cartWebEnd();
}
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");
}
static void webStartWrapperDetailedInternal(struct cart *theCart,
char *db, char *headerText, char *textOutBuf,
boolean withHttpHeader, boolean withLogo, boolean skipSectionHeader,
boolean withHtmlHeader)
/* output a CGI and HTML header with the given title in printf format */
{
char uiState[256];
char *scriptName = cgiScriptName();
boolean isEncode = FALSE;
if (theCart)
{
char *theGenome = NULL;
char *genomeEnc = NULL;
getDbAndGenome(theCart, &db, &theGenome, NULL);
genomeEnc = cgiEncode(theGenome);
safef(uiState, sizeof(uiState), "?%s=%s&%s=%s&%s=%s",
orgCgiName, genomeEnc,
dbCgiName, db,
cartSessionVarName(), cartSessionId(theCart));
}
else
{
uiState[0] = 0;
uiState[1] = 0;
}
if (db == NULL)
db = hDefaultDb();
boolean dbIsFound = hDbExists(db);
boolean haveBlat = FALSE;
if (dbIsFound)
haveBlat = hIsBlatIndexedDatabase(db);
if (scriptName == NULL)
scriptName = cloneString("");
/* don't output two headers */
if(webHeadAlreadyOutputed)
return;
if (sameString(cgiUsualString("action",""),"encodeReleaseLog") ||
rStringIn("EncodeDataVersions", scriptName))
isEncode = TRUE;
/* Preamble. */
dnaUtilOpen();
if (withHttpHeader)
puts("Content-type:text/html\n");
if (withHtmlHeader)
{
char *newString, *ptr1, *ptr2;
char *browserVersion;
if (btIE == cgiClientBrowser(&browserVersion, NULL, NULL) && *browserVersion < '8')
puts("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 3.2//EN\">");
else
puts("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Transitional//EN\" "
"\"http://www.w3.org/TR/html4/loose.dtd\">");
// Strict would be nice since it fixes atleast one IE problem (use of :hover CSS pseudoclass)
puts(
"<HTML>" "\n"
"<HEAD>" "\n"
);
printf("\t%s\n", headerText);
webPragmasEtc();
printf("\t<TITLE>");
/* we need to take any HTML formatting out of the titlebar string */
newString = cloneString(textOutBuf);
for(ptr1=newString, ptr2=textOutBuf; *ptr2 ; ptr2++)
{
if (*ptr2 == '<')
{
for(; *ptr2 && (*ptr2 != '>'); ptr2++)
;
}
else
*ptr1++ = *ptr2;
}
*ptr1 = 0;
htmlTextOut(newString);
printf(" </TITLE>\n ");
webIncludeResourceFile("HGStyle.css");
if (extraStyle != NULL)
puts(extraStyle);
printf("</HEAD>\n");
printBodyTag(stdout);
htmlWarnBoxSetup(stdout);// Sets up a warning box which can be filled with errors as they occur
puts(commonCssStyles());
}
webStartSectionTables();
if (withLogo)
{
puts("<TR><TH COLSPAN=1 ALIGN=\"left\">");
if (isEncode)
{
puts("<A HREF=\"http://www.genome.gov/10005107\" TARGET=\"_BLANK\">"
"<IMG SRC=\"../images/ENCODE_scaleup_logo.png\" height=50 ALT=\"ENCODE Project at NHGRI\">"
"</A>");
puts("<IMG SRC=\"../images/encodeDcc.jpg\" ALT=\"ENCODE Project at UCSC\">");
}
else
{
puts("<IMG SRC=\"../images/title.jpg\">");
}
puts("</TH></TR>" "\n"
"" "\n" );
}
/* Put up the hot links bar. */
char *menuStr = menuBar(theCart, db);
if(menuStr)
{
puts(menuStr);
}
if(!skipSectionHeader)
/* this HTML must be in calling code if skipSectionHeader is TRUE */
{
webFirstSection(textOutBuf);
};
webPushErrHandlers();
/* set the flag */
webHeadAlreadyOutputed = TRUE;
errAbortSetDoContentType(FALSE);
} /* static void webStartWrapperDetailedInternal() */
