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() */