void smallBreak() /* Draw small horizontal break */ { hPrintf("<FONT SIZE=1><BR></FONT>\n"); }
void modBaseAnchor(char *swissProtAcc) /* Print out anchor to modBase. */ { hPrintf("<A HREF=\"http://salilab.org/modbase/search?databaseID=%s\" TARGET=_blank>", swissProtAcc); //hPrintf("<A HREF=\"http://salilab.org/modbase-cgi/model_search.cgi?searchkw=name&kword=%s\" TARGET=_blank>", swissProtAcc); }
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); } }
void stringStatRow(char *label, char *val) /* Print label, string value. */ { hPrintf("<TR><TD>%s</TD><TD ALIGN=RIGHT>%s</TD></TR>\n", label, val); }
static void configControlPanel() /* Put up configuration control panel. */ { //struct userSettings *us = colUserSettings(); controlPanelStart(); hPrintf("<TABLE BORDER=0 CELLSPACING=1 CELLPADDING=1>\n"); hPrintf("<TR><TD ALIGN=LEFT>"); cgiMakeButton("submit", "submit"); hPrintf("</TD><TD> "); hPrintf("</TD><TD> "); hPrintf("</TD><TD>"); hPrintf("Columns:"); hPrintf("</TD><TD> "); cgiMakeButton(hideAllConfName, "hide all"); hPrintf("</TD><TD>"); cgiMakeButton(showAllConfName, "show all"); hPrintf("</TD><TD>"); cgiMakeButton(defaultConfName, "default"); hPrintf("</TD><TD>"); //hPrintf("Settings:"); //hPrintf("</TD><TD>"); //cgiMakeButton(saveCurrentConfName, "save"); //hPrintf("</TD><TD>"); //cgiMakeOptionalButton(useSavedConfName, "load", !userSettingsAnySaved(us)); hPrintf("</TD></TR></TABLE>"); //hPrintf("<TABLE BORDER=0 CELLSPACING=1 CELLPADDING=1>\n"); //hPrintf("<TR><TD ALIGN=LEFT>"); //hPrintf("Expression ratio colors: "); //hgExpColorDropDown(cart, expRatioColorVarName); //hPrintf("</TD><TD>"); //hPrintf("Show all splicing variants: "); //cgiMakeCheckBox(showAllSpliceVarName, // cartUsualBoolean(cart, showAllSpliceVarName, FALSE)); //hPrintf("</TD><TD>"); //cgiMakeButton(customPageDoName, "custom columns"); //hPrintf("</TD></TR></TABLE>"); controlPanelEnd(); }
static void searchAllColumns(struct sqlConnection *conn, struct column *colList, char *search) /* Call search on each column. */ { struct column *col; struct searchResult *srList, *sr; struct columnSearchResults *csrList = NULL, *csr; int totalCount = 0; struct searchResult *srOne = NULL; for (col = colList; col != NULL; col = col->next) { if (col->simpleSearch) { srList = col->simpleSearch(col, conn, search); if (showOnlyCanonical() && srList != NULL) { transformToCanonical(srList, conn); srList = removeDupes(srList); } if (srList != NULL) { srOne = srList; fillInMissingLabels(conn, colList, srList); AllocVar(csr); csr->label = columnSetting(col, "searchLabel", col->longLabel); csr->results = srList; slAddTail(&csrList, csr); totalCount += slCount(srList); } } } if (totalCount == 0) { displayData(conn, colList, NULL); if (anyWild(search)) warn("Sorry, the search box doesn't take wildcards, " "though in most cases it will find things without " "them. Try entering your search without * or ? " "characters."); else warn("Sorry, couldn't find '%s'", search); } else if (totalCount == 1 || allSame(csrList)) // else if (totalCount == 1) displayData(conn, colList, &srOne->gp); else { makeTitle("Simple Search Results", NULL); for (csr = csrList; csr != NULL; csr = csr->next) { hPrintf("<H2>%s</H2>\n", csr->label); slSort(&csr->results, searchResultCmpShortLabel); for (sr = csr->results; sr != NULL; sr = sr->next) { selfAnchorSearch(&sr->gp); if (sr->matchingId != NULL) hPrintf("%s (%s)", sr->matchingId, sr->shortLabel); else hPrintf("%s", sr->shortLabel); hPrintf("</A> - %s<BR>\n", sr->longLabel); } } } }
void configMultiRegionPage() /* Do multi-region config page after setting track visibility. If vis is -2, then visibility * is unchanged. If -1 then set visibility to default, otherwise it should * be tvHide, tvDense, etc. */ { char *groupTarget; struct track *trackList; struct track *ideoTrack; struct group *groupList; int vis = -2; configInitTrackList(vis, &groupTarget, &trackList, &ideoTrack, &groupList); hPrintf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=%s>\n", hgTracksName(), cartUsualString(cart, "formMethod", "POST")); webStartWrapperDetailedNoArgs(cart, database, "", "", FALSE, FALSE, FALSE, FALSE); cartSaveSession(cart); hPrintf("<BR>\n"); hTableStart(); virtModeType = cartUsualString(cart, "virtModeType", virtModeType); hPrintf("<TR><TD>"); cgiMakeRadioButton("virtModeType", "default", sameWord("default", virtModeType)); hPrintf("</TD><TD>"); hPrintf("Exit multi-region mode"); hPrintf("</TD></TR>\n"); struct sqlConnection *conn = NULL; if (!trackHubDatabase(database)) // no db conn for assembly hubs conn = hAllocConn(database); // Do we have a gene table for exonMostly? findBestEMGeneTable(trackList); if (emGeneTable) { hPrintf("<TR><TD>"); cgiMakeRadioButton("virtModeType", "exonMostly", sameWord("exonMostly", virtModeType)); hPrintf("</TD><TD>"); hPrintf("Show exons using %s. Use padding of: ", emGeneTrack->shortLabel); hIntVar("emPadding", cartUsualInt(cart, "emPadding", emPadding), 3); hPrintf(" bases."); hPrintf("</TD></TR>\n"); } if (emGeneTable) { hPrintf("<TR><TD>"); cgiMakeRadioButton("virtModeType", "geneMostly", sameWord("geneMostly", virtModeType)); hPrintf("</TD><TD>"); hPrintf("Show genes using %s. Use padding of: ", emGeneTrack->shortLabel); hIntVar("gmPadding", cartUsualInt(cart, "gmPadding", gmPadding), 3); hPrintf(" bases."); hPrintf("</TD></TR>\n"); } /* obsolete if (conn && sqlTableExists(conn,"knownCanonical")) { hPrintf("<TR><TD>"); cgiMakeRadioButton("virtModeType", "kcGenes", sameWord("kcGenes", virtModeType)); hPrintf("</TD><TD>"); hPrintf("Show gene regions genome-wide."); hPrintf("</TD></TR>\n"); } */ hPrintf("<TR><TD>"); cgiMakeRadioButton("virtModeType", "customUrl", sameWord("customUrl", virtModeType)); hPrintf("</TD><TD>"); hPrintf("Enter Custom regions as BED, or a URL to them:<br>"); multiRegionsBedUrl = cartUsualString(cart, "multiRegionsBedUrl", multiRegionsBedUrl); struct dyString *dyMultiRegionsBedInput = dyStringNew(256); if (strstr(multiRegionsBedUrl,"://")) { dyStringAppend(dyMultiRegionsBedInput, multiRegionsBedUrl); } else { if (fileExists(multiRegionsBedUrl)) { struct lineFile *lf = lineFileMayOpen(multiRegionsBedUrl, TRUE); char *line; int lineSize; while (lineFileNext(lf, &line, &lineSize)) { dyStringPrintf(dyMultiRegionsBedInput, "%s\n", line); } lineFileClose(&lf); } } hPrintf("<TEXTAREA NAME='multiRegionsBedInput' ID='multiRegionsBedInput' rows='4' cols='58' style='white-space: pre;'>%s</TEXTAREA>", dyMultiRegionsBedInput->string); hPrintf("</TD></TR>\n"); /* The AllChroms option will be released in future if (emGeneTable && sqlTableExists(conn, emGeneTable)) { hPrintf("<TR><TD>"); cgiMakeRadioButton("virtModeType", "singleTrans", sameWord("singleTrans", virtModeType)); hPrintf("</TD><TD>"); hPrintf("Show only one transcript using an ID from %s : ", emGeneTrack->shortLabel); char *trans = cartUsualString(cart, "singleTransId", singleTransId); char sql[1024]; sqlSafef(sql, sizeof sql, "select name from %s where name='%s'", emGeneTable, trans); char *result = sqlQuickString(conn, sql); if (!result) { sqlSafef(sql, sizeof sql, "select name from %s limit 1", emGeneTable); trans = sqlQuickString(conn, sql); } hTextVar("singleTransId", trans, 20); hPrintf("</TD></TR>\n"); } */ if (conn) { boolean altLocExists = sqlTableExists(conn, "altLocations"); boolean fixLocExists = sqlTableExists(conn, "fixLocations"); if (altLocExists || fixLocExists) { hPrintf("<TR><TD>"); cgiMakeRadioButton("virtModeType", "singleAltHaplo", sameWord("singleAltHaplo", virtModeType)); hPrintf("</TD><TD>"); hPrintf("Show one alternate haplotype"); if (fixLocExists) hPrintf(" or fix patch"); hPrintf(", placed on its chromosome, using ID: "); char *haplo = cartUsualString(cart, "singleAltHaploId", singleAltHaploId); char *foundHaplo = NULL; char sql[1024]; if (altLocExists) { sqlSafef(sql, sizeof sql, "select name from altLocations where name rlike '^%s(:[0-9-]+)?'", haplo); foundHaplo = sqlQuickString(conn, sql); } if (!foundHaplo && fixLocExists) { sqlSafef(sql, sizeof sql, "select name from fixLocations where name rlike '^%s(:[0-9-]+)?'", haplo); foundHaplo = sqlQuickString(conn, sql); } if (!foundHaplo) { if (altLocExists) sqlSafef(sql, sizeof sql, "select name from altLocations limit 1"); else sqlSafef(sql, sizeof sql, "select name from fixLocations limit 1"); haplo = sqlQuickString(conn, sql); chopSuffixAt(haplo, ':'); } hTextVar("singleAltHaploId", haplo, 60); hPrintf("</TD></TR>\n"); } } /* disable demo for now if (sameString(database,"hg19") || sameString(database, "hg38")) { hPrintf("<TR><TD>"); cgiMakeRadioButton("virtModeType", "demo1", sameWord("demo1", virtModeType)); hPrintf("</TD><TD>"); hPrintf("demo1 two windows on two chroms (default pos on chr21, and same loc on chr22)"); hPrintf("</TD></TR>\n"); } */ /* Disabled for now hPrintf("<TR><TD>"); cgiMakeRadioButton("virtModeType", "demo2", sameWord("demo2", virtModeType)); hPrintf("</TD><TD>"); hPrintf("demo2 multiple "); hIntVar("demo2NumWindows", cartUsualInt(cart, "demo2NumWindows", demo2NumWindows), 3); hPrintf(" windows on one chrom chr21 def posn, window size "); hIntVar("demo2WindowSize", cartUsualInt(cart, "demo2WindowSize", demo2WindowSize), 3); hPrintf(" and step size "); hIntVar("demo2StepSize", cartUsualInt(cart, "demo2StepSize", demo2StepSize), 3); hPrintf(" exon-like"); hPrintf("</TD></TR>\n"); */ /* The AllChroms option will be released in future if (conn) // requires chromInfo from database. { // TODO allow it to use assembly hubs via trackHubAllChromInfo() ? hPrintf("<TR><TD>"); cgiMakeRadioButton("virtModeType", "allChroms", sameWord("allChroms", virtModeType)); hPrintf("</TD><TD>"); hPrintf("<br>Show all chromosomes.<br><span style='color:red'>Warning:</span> Turn off all tracks except bigBed, bigWig, and very sparse tracks.<br>Press Hide All to hide all tracks."); hPrintf("</TD></TR>\n"); } */ /* Disabled for now hPrintf("<TR><TD>"); cgiMakeRadioButton("virtModeType", "demo4", sameWord("demo4", virtModeType)); hPrintf("</TD><TD>"); hPrintf("demo4 multiple (311) windows showing exons from TITIN gene uc031rqd.1."); hPrintf("</TD></TR>\n"); */ /* Disabled for now hPrintf("<TR><TD>"); cgiMakeRadioButton("virtModeType", "demo5", sameWord("demo5", virtModeType)); hPrintf("</TD><TD>"); hPrintf("demo5 alt locus on hg38. Shows alt chrom surrounded by regions of same size from reference genome."); hPrintf("</TD></TR>\n"); */ /* Disabled for now hPrintf("<TR><TD>"); cgiMakeRadioButton("virtModeType", "demo6", sameWord("demo6", virtModeType)); hPrintf("</TD><TD>"); hPrintf("demo6 shows zoomed in exon-exon junction from SOD1 gene, between exon1 and exon2."); hPrintf("</TD></TR>\n"); */ hTableEnd(); hPrintf("<BR>\n"); hPrintf("<TABLE style=\"border:0px; \">\n"); hPrintf("<TR><TD>"); hCheckBox("emAltHighlight", cartUsualBoolean(cart, "emAltHighlight", FALSE)); hPrintf("</TD><TD>"); hPrintf("Highlight alternating regions in multi-region view"); hPrintf("</TD></TR>\n"); hPrintf("</TABLE>\n"); hPrintf("<BR>\n"); hPrintf("<TABLE style=\"border:0px;width:650px \">\n"); hPrintf("<TR><TD>"); cgiMakeButton("topSubmit", "submit"); hPrintf("</TD><TD align=right>"); hPrintf("<A HREF=\"../goldenPath/help/multiRegionHelp.html\" target=_blank>Help</A>\n"); hPrintf("</TD></TR>\n"); hPrintf("</TABLE>\n"); hFreeConn(&conn); cgiDown(0.9); freez(&groupTarget); webEndSectionTables(); hPrintf("</FORM>"); }
void verifyGreatAssemblies() { // First read in the assembly name and description information into name lists struct slName* supportedAssemblies = NULL; struct lineFile *lf = lineFileOpen(greatData, TRUE); int fieldCount = 1; char* row[fieldCount]; int wordCount; while ((wordCount = lineFileChopTab(lf, row)) != 0) { if (wordCount != fieldCount) errAbort("The %s file is not properly formatted.\n", greatData); slNameAddHead(&supportedAssemblies, row[0]); } lineFileClose(&lf); boolean invalidAssembly = TRUE; struct slName* currAssembly; for (currAssembly = supportedAssemblies; currAssembly != NULL; currAssembly = currAssembly->next) { if (!hDbIsActive(currAssembly->name)) { errAbort("Assembly %s in supported assembly file is not an active assembly.\n", currAssembly->name); } if (sameOk(database, currAssembly->name)) { invalidAssembly = FALSE; break; } } if (invalidAssembly) { slReverse(&supportedAssemblies); currAssembly = supportedAssemblies; struct dyString* dy = dyStringNew(0); addAssemblyToSupportedList(dy, currAssembly->name); currAssembly = currAssembly->next; while (currAssembly != NULL) { dyStringAppend(dy, ", "); if (currAssembly->next == NULL) dyStringAppend(dy, "and "); addAssemblyToSupportedList(dy, currAssembly->name); currAssembly = currAssembly->next; } hPrintf("<script type='text/javascript'>\n"); hPrintf("function logSpecies() {\n"); hPrintf("try {\n"); hPrintf("var r = new XMLHttpRequest();\n"); hPrintf("r.open('GET', 'http://great.stanford.edu/public/cgi-bin/logSpecies.php?species=%s');\n", database); hPrintf("r.send(null);\n"); hPrintf("} catch (err) { }\n"); hPrintf("}\n"); hPrintf("window.onload = logSpecies;\n"); hPrintf("</script>\n"); errAbort("GREAT only supports the %s assemblies." "\nPlease go back and ensure that one of those assemblies is chosen.", dyStringContents(dy)); htmlClose(); dyStringFree(&dy); } slNameFreeList(&supportedAssemblies); }
static void rnaStructurePrint(struct section *section, struct sqlConnection *conn, char *geneId) /* Print out rnaStructure table. */ { static boolean firstTime = TRUE; static char *names[2] = {"5' UTR", "3' UTR"}; static char *tables[2] = {"foldUtr5", "foldUtr3"}; int side; if (firstTime) { rnaTrashDirsInit(tables, ArraySize(tables)); firstTime = FALSE; } webPrintLinkTableStart(); webPrintLabelCell("Region"); webPrintLabelCell("Fold Energy"); webPrintLabelCell("Bases"); webPrintLabelCell("Energy/Base"); webPrintWideCenteredLabelCell("Display As", 3); for (side = 0; side < ArraySize(names); ++side) { char *table = tables[side]; struct sqlResult *sr; char query[256], **row; safef(query, sizeof(query), "select * from %s where name = '%s'", table, geneId); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { struct rnaFold fold; int bases; char psName[128]; /* Load fold and save it as postScript. */ rnaFoldStaticLoad(row, &fold); safef(psName, sizeof(psName), "../trash/%s/%s_%s.ps", table, table, geneId); if (!fileExists(psName)) { FILE *f; f = popen("../cgi-bin/RNAplot", "w"); if (f != NULL) { fprintf(f, ">%s\n", psName); /* This tells where to put file. */ fprintf(f, "%s\n%s\n", fold.seq, fold.fold); pclose(f); } } /* Print row of table, starting with energy terms . */ hPrintf("</TR><TR>"); bases = strlen(fold.seq); webPrintLinkCell(names[side]); webPrintLinkCellStart(); hPrintf("%1.2f", fold.energy); webPrintLinkCellEnd(); webPrintLinkCellStart(); hPrintf("%d", bases); webPrintLinkCellEnd(); webPrintLinkCellStart(); hPrintf("%1.3f", fold.energy/bases); webPrintLinkCellEnd(); /* Print link to png image. */ webPrintLinkCellStart(); hPrintf("<A HREF=\"%s?%s&%s=%s&%s=%s&%s=%s\" class=\"toc\" TARGET=_blank>", geneCgi, cartSidUrlString(cart), hggMrnaFoldRegion, table, hggMrnaFoldPs, psName, hggDoRnaFoldDisplay, "picture"); hPrintf(" Picture "); hPrintf("</A>"); webPrintLinkCellEnd(); /* Print link to PostScript. */ webPrintLinkCellStart(); hPrintf("<A HREF=\"%s\" class=\"toc\">", psName); hPrintf(" PostScript "); hPrintf("</A>"); webPrintLinkCellEnd(); /* Print link to text. */ webPrintLinkCellStart(); hPrintf("<A HREF=\"%s?%s&%s=%s&%s=%s\" class=\"toc\" TARGET=_blank>", geneCgi, cartSidUrlString(cart), hggMrnaFoldRegion, table, hggDoRnaFoldDisplay, "text"); hPrintf(" Text "); hPrintf("</A>"); webPrintLinkCellEnd(); } sqlFreeResult(&sr); } webPrintLinkTableEnd(); hPrintf("<BR>The RNAfold program from the "); hPrintf("<A HREF=\"http://www.tbi.univie.ac.at/~ivo/RNA/\" TARGET=_blank>"); hPrintf("Vienna RNA Package</A> is used to perform the "); hPrintf("secondary structure predictions and folding calculations. "); hPrintf("The estimated folding energy is in kcal/mol. The more "); hPrintf("negative the energy, the more secondary structure the RNA "); hPrintf("is likely to have."); }
void showSchemaBam(char *table, struct trackDb *tdb) /* Show schema on bam. */ { struct sqlConnection *conn = NULL; if (!trackHubDatabase(database)) conn = hAllocConn(database); char *fileName = bamFileName(table, conn, NULL); struct asObject *as = bamAsObj(); hPrintf("<B>Database:</B> %s", database); hPrintf(" <B>Primary Table:</B> %s<br>", table); hPrintf("<B>BAM File:</B> %s", fileName); hPrintf("<BR>\n"); hPrintf("<B>Format description:</B> %s<BR>", as->comment); hPrintf("See the <A HREF=\"%s\" target=_blank>SAM Format Specification</A> for more details<BR>\n", "http://samtools.sourceforge.net/SAM1.pdf"); /* Put up table that describes fields. */ hTableStart(); hPrintf("<TR><TH>field</TH>"); hPrintf("<TH>description</TH> "); puts("</TR>\n"); struct asColumn *col; int colCount = 0; for (col = as->columnList; col != NULL; col = col->next) { hPrintf("<TR><TD><TT>%s</TT></TD>", col->name); hPrintf("<TD>%s</TD></TR>", col->comment); ++colCount; } hTableEnd(); /* Put up another section with sample rows. */ webNewSection("Sample Rows"); hTableStart(); /* Print field names as column headers for example */ hPrintf("<TR>"); int colIx = 0; for (col = as->columnList; col != NULL; col = col->next) { hPrintf("<TH>%s</TH>", col->name); ++colIx; } hPrintf("</TR>\n"); /* Fetch sample rows. */ samfile_t *fh = bamOpen(fileName, NULL); struct lm *lm = lmInit(0); struct samAlignment *sam, *samList = bamReadNextSamAlignments(fh, 10, lm); /* Print sample lines. */ char *row[SAMALIGNMENT_NUM_COLS]; char numBuf[BAM_NUM_BUF_SIZE]; for (sam=samList; sam != NULL; sam = sam->next) { samAlignmentToRow(sam, numBuf, row); hPrintf("<TR>"); for (colIx=0; colIx<colCount; ++colIx) { hPrintf("<TD>"); xmlEscapeStringToFile(row[colIx], stdout); hPrintf("</TD>"); } hPrintf("</TR>\n"); } hTableEnd(); printTrackHtml(tdb); /* Clean up and go home. */ bamClose(&fh); lmCleanup(&lm); freeMem(fileName); hFreeConn(&conn); }
static void otherOrgsPrint(struct section *section, struct sqlConnection *conn, char *geneId) /* Print the otherOrgs section. */ { struct otherOrg *otherOrg, *otherOrgList = section->items; hPrintf( "Orthologies between human, mouse, and rat are computed by taking the " "best BLASTP hit, and filtering out non-syntenic hits. For " "more distant species reciprocal-best BLASTP hits are used. " "Note that the absence of an ortholog in the table below may " "reflect incomplete annotations in the other species rather than " "a true absence of the orthologous gene."); webPrintLinkTableStart(); for (otherOrg = otherOrgList; otherOrg != NULL; otherOrg = otherOrg->next) webPrintLabelCell(otherOrg->shortLabel); hPrintf("</TR>\n<TR>"); for (otherOrg = otherOrgList; otherOrg != NULL; otherOrg = otherOrg->next) { char *pos = otherOrgPosition(otherOrg, conn, geneId); otherOrgPrintLink(otherOrg, "Genome Browser", "No ortholog", TRUE, pos, otherOrg->genomeUrl); freeMem(pos); } hPrintf("</TR>\n<TR>"); for (otherOrg = otherOrgList; otherOrg != NULL; otherOrg = otherOrg->next) { char *id = otherOrgId(otherOrg, conn, geneId); otherOrgPrintLink(otherOrg, "Gene Details", " ", TRUE, id, otherOrg->geneUrl); freeMem(id); } hPrintf("</TR>\n<TR>"); for (otherOrg = otherOrgList; otherOrg != NULL; otherOrg = otherOrg->next) { char *id = otherOrgId(otherOrg, conn, geneId); otherOrgPrintLink(otherOrg, "Gene Sorter", " ", TRUE, id, otherOrg->sorterUrl); freeMem(id); } hPrintf("</TR>\n<TR>"); for (otherOrg = otherOrgList; otherOrg != NULL; otherOrg = otherOrg->next) { char *id = otherOrgId(otherOrg, conn, geneId); id = otherOrgExternalId(otherOrg, id); otherOrgPrintLink(otherOrg, otherOrg->otherName, " ", FALSE, id, otherOrg->otherUrl); freeMem(id); } hPrintf("</TR>\n<TR>"); for (otherOrg = otherOrgList; otherOrg != NULL; otherOrg = otherOrg->next) { char *id = otherOrgProteinId(otherOrg, conn, geneId); otherOrgPepLink(otherOrg, hggDoOtherProteinSeq, "Protein Sequence", id, conn); freeMem(id); } hPrintf("</TR>\n<TR>"); for (otherOrg = otherOrgList; otherOrg != NULL; otherOrg = otherOrg->next) { char *id = otherOrgProteinId(otherOrg, conn, geneId); otherOrgPepLink(otherOrg, hggDoOtherProteinAli, "Alignment", id, conn); freeMem(id); } webPrintLinkTableEnd(); }
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 sortGenes(struct sqlConnection *conn) /* Put up sort gene page. */ { cartWebStart(cart, database, "Finding Candidate Genes for Gene Sorter"); if (!hgNearOk(database)) errAbort("Sorry, gene sorter not available for this database."); /* Get list of regions. */ struct genoGraph *gg = ggFirstVisible(); double threshold = getThreshold(); struct bed3 *bed, *bedList = regionsOverThreshold(gg); /* Figure out what table and column are the sorter's main gene set. */ struct hash *genomeRa = hgReadRa(genome, database, "hgNearData", "genome.ra", NULL); char *geneTable = hashMustFindVal(genomeRa, "geneTable"); char *idColumn = hashMustFindVal(genomeRa, "idColumn"); /* if marker labels were present when the file was uploaded, they are saved here */ char cgmName[256]; safef(cgmName, sizeof(cgmName), "%s.cgm", gg->binFileName); struct lineFile *m = lineFileMayOpen(cgmName, TRUE); char *cgmRow[4]; cgmRow[0] = ""; /* dummy row */ cgmRow[1] = ""; cgmRow[2] = "0"; cgmRow[3] = "0"; FILE *g = NULL; int markerCount = 0; struct tempName snpTn; if (m) { /* Create custom column output file. */ trashDirFile(&snpTn, "hgg", "marker", ".mrk"); g = mustOpen(snpTn.forCgi, "w"); fprintf(g, "column name=\"%s Markers\" shortLabel=\"%s Markers over threshold\" longLabel=\"%s Markers in regions over threshold\" " "visibility=on priority=99 " "\n" , gg->shortLabel , gg->shortLabel , gg->shortLabel ); } /*** Build up hash of all transcriptHash that are in region. */ struct hash *transcriptHash = hashNew(16); /* This loop handles one chromosome at a time. It depends on * the bedList being sorted by chromosome. */ for (bed = bedList; bed != NULL; ) { /* Make binKeeper and stuff in all regions in this chromosome into it. */ char *chrom = bed->chrom; int chromSize = hChromSize(database, chrom); struct binKeeper *bk = binKeeperNew(0, chromSize); while (bed != NULL && sameString(chrom, bed->chrom)) { binKeeperAdd(bk, bed->chromStart, bed->chromEnd, bed); bed = bed->next; } struct binKeeper *bkGenes = NULL; if (m) bkGenes = binKeeperNew(0, chromSize); /* Query database to find out bounds of all genes on this chromosome * and if they overlap any of the regions then put them in the hash. */ char query[512]; safef(query, sizeof(query), "select name,txStart,txEnd from %s where chrom='%s'", geneTable, chrom); struct sqlResult *sr = sqlGetResult(conn, query); char **row; while ((row = sqlNextRow(sr)) != NULL) { char *name = row[0]; int start = sqlUnsigned(row[1]); int end = sqlUnsigned(row[2]); if (binKeeperAnyOverlap(bk, start, end)) { hashStore(transcriptHash, name); if (m) binKeeperAdd(bkGenes, start, end, cloneString(name)); } } sqlFreeResult(&sr); if (m) { /* Read cgm file if it exists, looking at all markers on this chromosome * and if they overlap any of the regions and genes then output them. */ do { // marker, chrom, chromStart, val char *marker = cgmRow[0]; char *chr = cgmRow[1]; int start = sqlUnsigned(cgmRow[2]); int end = start+1; double val = sqlDouble(cgmRow[3]); int cmp = strcmp(chr,chrom); if (cmp > 0) break; if (cmp == 0) { if (val >= threshold) { struct binElement *el, *bkList = binKeeperFind(bkGenes, start, end); for (el = bkList; el; el=el->next) { /* output to custom column trash file */ fprintf(g, "%s %s\n", (char *)el->val, marker); } if (bkList) { ++markerCount; slFreeList(&bkList); } } } } while (lineFileRow(m, cgmRow)); } /* Clean up for this chromosome. */ binKeeperFree(&bk); if (m) { /* For speed, we do not free up the values (cloned the kg names earlier) */ binKeeperFree(&bkGenes); } } /* Get list of all transcripts in regions. */ struct hashEl *el, *list = hashElListHash(transcriptHash); /* Create file with all matching gene IDs. */ struct tempName keyTn; trashDirFile(&keyTn, "hgg", "key", ".key"); FILE *f = mustOpen(keyTn.forCgi, "w"); for (el = list; el != NULL; el = el->next) fprintf(f, "%s\n", el->name); carefulClose(&f); /* Print out some info. */ hPrintf("Thresholding <i>%s</i> at %g. ", gg->shortLabel, threshold); hPrintf("There are %d regions covering %lld bases.<BR>\n", slCount(bedList), bedTotalSize((struct bed*)bedList) ); hPrintf("Installed a Gene Sorter filter that selects only genes in these regions.<BR>\n"); if (m) { hPrintf("There are %d markers in the regions over threshold that overlap knownGenes.<BR>\n", markerCount); hPrintf("Installed a Gene Sorter custom column called \"%s Markers\" with these markers.<BR>\n", gg->shortLabel); } /* close custom column output file */ if (m) { lineFileClose(&m); carefulClose(&g); } /* Stuff cart variable with name of file. */ char keyCartName[256]; safef(keyCartName, sizeof(keyCartName), "%s%s.keyFile", advFilterPrefix, idColumn); cartSetString(cart, keyCartName, keyTn.forCgi); cartSetString(cart, customFileVarName, snpTn.forCgi); char snpVisCartNameTemp[256]; char *snpVisCartName = NULL; safef(snpVisCartNameTemp, sizeof(snpVisCartNameTemp), "%s%s Markers.vis", colConfigPrefix, gg->shortLabel); snpVisCartName = replaceChars(snpVisCartNameTemp, " ", "_"); cartSetString(cart, snpVisCartName, "1"); freeMem(snpVisCartName); hPrintf("<FORM ACTION=\"../cgi-bin/hgNear\" METHOD=GET>\n"); cartSaveSession(cart); hPrintf("<CENTER>"); cgiMakeButton("submit", "go to gene sorter"); hPrintf("</CENTER>"); hPrintf("</FORM>"); cartWebEnd(); }
void makeActiveImagePB(char *psOutput, char *psOutput2) /* Make image and image map. */ { char *mapName = "map"; int pixWidth, pixHeight; struct sqlConnection *conn; char query[256]; struct sqlResult *sr; char **row; int iypos; char *spDisplayId; char *oldDisplayId; conn = sqlConnect(UNIPROT_DB_NAME); printf("<BR>"); hPrintf("<BR><font size=4><B>Protein: "); hPrintf("%s</B>", proteinID); /* Please note the hiv database name is hard wired here.*/ safef(query, sizeof(query), "select subjId from hivVax003Vax004.gsIdXref where aaSeqId = '%s'", proteinID); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { printf("<BR>"); hPrintf("<font size=4><B>Subject: "); hPrintf("<A HREF=\"../cgi-bin/gsidSubj?hgs_subj=%s&submit=Go!\">", row[0]); hPrintf("%s</A></B><BR>", row[0]); } sqlFreeResult(&sr); spDisplayId = spAccToId(conn, spFindAcc(conn, proteinID)); if (strstr(spDisplayId, spFindAcc(conn, proteinID)) == NULL) { hPrintf(" (aka %s", spDisplayId); /* show once if the new and old displayId are the same */ oldDisplayId = oldSpDisplayId(spDisplayId); if (oldDisplayId != NULL) { if (!sameWord(spDisplayId, oldDisplayId)) { hPrintf(" or %s", oldSpDisplayId(spDisplayId)); } } hPrintf(")\n"); } hPrintf("</font><br>"); protSeq = getAA(proteinID); if (protSeq == NULL) { errAbort("%s is not a current valid entry in UniProt(SWISS-PROT/TrEMBL)\n", proteinID); } protSeqLen = strlen(protSeq); fflush(stdout); iypos = 15; doTracks(proteinID, mrnaID, protSeq, &iypos, psOutput); if (!hTableExists(database, "pbStamp")) goto histDone; pbScale = 3; pixWidth = 520; insideWidth = pixWidth-gfxBorder; pixHeight = 350; if (psOutput2) { vg2 = vgOpenPostScript(pixWidth, pixHeight, psOutput2); } else { trashDirFile(&gifTn2, "pbt", "pbt", ".gif"); vg2 = vgOpenGif(pixWidth, pixHeight, gifTn2.forCgi, FALSE); } g_vg = vg2; pbRed = vgFindColorIx(vg2, 0xf9, 0x51, 0x59); pbBlue = vgFindColorIx(g_vg, 0x00, 0x00, 0xd0); normalColor = pbBlue; abnormalColor = pbRed; bkgColor = vgFindColorIx(vg2, 255, 254, 232); vgBox(vg2, 0, 0, insideWidth, pixHeight, bkgColor); /* Start up client side map. */ mapName=cloneString("pbStamps"); hPrintf("\n<MAP Name=%s>\n", mapName); vgSetClip(vg2, 0, gfxBorder, insideWidth, pixHeight - 2*gfxBorder); iypos = 15; /* Draw stamps. */ doStamps(proteinID, mrnaID, protSeq, vg2, &iypos); /* Finish map. */ hPrintf("</MAP>\n"); /* Save out picture and tell html file about it. */ vgClose(&vg2); hPrintf("<P>"); hPrintf("\n<IMG SRC=\"%s\" BORDER=1 WIDTH=%d HEIGHT=%d USEMAP=#%s><BR>", gifTn2.forCgi, pixWidth, pixHeight, mapName); if (proteinInSupportedGenome) { hPrintf("\n<A HREF=\"../goldenPath/help/pbTracksHelpFiles/pbTracksHelp.shtml#histograms\" TARGET=_blank>"); } else { hPrintf("\n<A HREF=\"../goldenPath/help/pbTracksHelpFiles/pbGsid/pbTracksHelp.shtml#histograms\" TARGET=_blank>"); } hPrintf("Explanation of Protein Property Histograms</A><BR>"); hPrintf("<P>"); histDone: hPrintf("<P>"); fflush(stdout); printFASTA(proteinID, protSeq); }
static void mainControlPanel() /* Make control panel. */ { controlPanelStart(); /* advFilter, configure buttons */ { cgiMakeButton(confVarName, "configure"); hPrintf(" "); if (gotAdvFilter()) cgiMakeButton(advFilterVarName, "filter (now on)"); else cgiMakeButton(advFilterVarName, "filter (now off)"); hPrintf(" "); } /* Do items to display drop-down */ { int i=0; static char *menu[] = {"25", "50", "100", "200", "500", "1000", "all"}; hPrintf(" display "); hPrintf("<SELECT NAME=\"%s\"", countVarName); hPrintf(" onchange=\"document.mainForm.submit();\">\n"); for (i = 0; i < ArraySize(menu); ++i) { hPrintf("<OPTION VALUE=\"%s\"", menu[i]); if (sameString(menu[i], displayCountString)) hPrintf(" SELECTED"); hPrintf(">%s\n", menu[i]); } hPrintf("</SELECT>\n"); } /* Make getDna, getText buttons */ { hPrintf(" output "); cgiMakeOptionalButton(getSeqPageVarName, "sequence", FALSE); hPrintf(" "); cgiMakeOptionalButton(getTextVarName, "text", FALSE); } controlPanelEnd(); }
void configPageSetTrackVis(int vis) /* Do config page after setting track visibility. If vis is -2, then visibility * is unchanged. If -1 then set visibility to default, otherwise it should * be tvHide, tvDense, etc. */ { struct dyString *title = dyStringNew(0); char *groupTarget = NULL; struct track *trackList = NULL; struct track *ideoTrack = NULL; struct group *groupList = NULL; withPriorityOverride = cartUsualBoolean(cart, configPriorityOverride, FALSE); /* Get track list and group them. */ ctList = customTracksParseCart(database, cart, &browserLines, &ctFileName); trackList = getTrackList(&groupList, vis); /* The ideogram for some reason is considered a track. * We don't really want to process it as one though, so * we see if it's there, and if necessary remove it. */ ideoTrack = chromIdeoTrack(trackList); if (ideoTrack != NULL) removeTrackFromGroup(ideoTrack); /* Fetch group to change on if any from CGI, * and remove var so it doesn't get used again. */ groupTarget = cloneString(cartUsualString(cart, configGroupTarget, "")); cartRemove(cart, configGroupTarget); if (sameString(groupTarget, "none")) freez(&groupTarget); dyStringPrintf(title, "Configure Image"); hPrintf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=%s>\n", hgTracksName(), cartUsualString(cart, "formMethod", "POST")); webStartWrapperDetailedNoArgs(cart, database, "", title->string, FALSE, FALSE, FALSE, FALSE); cartSaveSession(cart); hPrintf("<INPUT TYPE=HIDDEN NAME=\"hgTracksConfigPage\" VALUE=\"\">"); /* do not want all the submit buttons named the same thing, this one is: */ cgiMakeButton("topSubmit", "submit"); // 3 column table hPrintf("<TABLE style=\"border:0px; \">\n"); hPrintf("<TR><TD>image width:"); hPrintf("<TD style=\"text-align: right\">"); hIntVar("pix", tl.picWidth, 4); hPrintf("<TD>pixels</TR>"); hPrintf("<TR><TD>label area width:"); hPrintf("<TD style=\"text-align: right\">"); hIntVar("hgt.labelWidth", leftLabelWidthChars, 2); hPrintf("<TD>characters<TD></TR>"); hPrintf("<TR><TD>text size:"); hPrintf("<TD style=\"text-align: right\">"); textSizeDropDown(); hPrintf("<TD>"); if (trackLayoutInclFontExtras()) { char *defaultStyle = cartUsualString(cart, "fontType", "medium"); cartMakeRadioButton(cart, "fontType", "medium", defaultStyle); hPrintf(" medium "); cartMakeRadioButton(cart, "fontType", "fixed", defaultStyle); hPrintf(" fixed "); cartMakeRadioButton(cart, "fontType", "bold", defaultStyle); hPrintf(" bold "); hPrintf(" "); } hPrintf("<TR><BR>"); hTableStart(); if (ideoTrack != NULL) { hPrintf("<TR><TD>"); hCheckBox("ideogram", cartUsualBoolean(cart, "ideogram", TRUE)); hPrintf("</TD><TD>"); hPrintf("Display chromosome ideogram above main graphic"); hPrintf("</TD></TR>\n"); } hPrintf("<TR><TD>"); hCheckBox("guidelines", cartUsualBoolean(cart, "guidelines", TRUE)); hPrintf("</TD><TD>"); hPrintf("Show light blue vertical guidelines"); hPrintf("</TD></TR>\n"); hPrintf("<TR><TD>"); hCheckBox("leftLabels", cartUsualBoolean(cart, "leftLabels", TRUE)); hPrintf("</TD><TD>"); hPrintf("Display labels to the left of items in tracks"); hPrintf("</TD></TR>\n"); hPrintf("<TR><TD>"); hCheckBox("centerLabels", cartUsualBoolean(cart, "centerLabels", TRUE)); hPrintf("</TD><TD>"); hPrintf("Display description above each track"); hPrintf("</TD></TR>\n"); hPrintf("<TR><TD>"); hCheckBox("trackControlsOnMain", cartUsualBoolean(cart, "trackControlsOnMain", TRUE)); hPrintf("</TD><TD>"); hPrintf("Show track controls under main graphic"); hPrintf("</TD></TR>\n"); hPrintf("<TR><TD>"); hCheckBox("nextItemArrows", cartUsualBoolean(cart, "nextItemArrows", FALSE)); hPrintf("</TD><TD>"); hPrintf("Next/previous item navigation"); hPrintf("</TD></TR>\n"); hPrintf("<TR><TD>"); hCheckBox("nextExonArrows", cartUsualBoolean(cart, "nextExonArrows", TRUE)); hPrintf("</TD><TD>"); hPrintf("Next/previous exon navigation"); hPrintf("</TD></TR>\n"); #ifdef PRIORITY_CHANGES_IN_CONFIG_UI hPrintf("<TR><TD>"); char *javascript="onClick=\"document.mainForm.hgTracksConfigPage.value='configure';document.mainForm.submit();\""; hCheckBoxJS(configPriorityOverride, cartUsualBoolean(cart, configPriorityOverride , FALSE), javascript); hPrintf("</TD><TD>"); hPrintf("Enable track re-ordering"); hPrintf("</TD></TR>\n"); #endif///def PRIORITY_CHANGES_IN_CONFIG_UI hPrintf("<TR><TD>"); hCheckBox("enableAdvancedJavascript", advancedJavascriptFeaturesEnabled(cart)); hPrintf("</TD><TD>"); hPrintf("Enable advanced javascript features"); hPrintf("</TD></TR>\n"); hTableEnd(); char *freeze = hFreezeFromDb(database); char buf[128]; if (stringIn(database, freeze)) safef(buf, sizeof buf, "Configure Tracks on %s %s: %s %s", organization, browserName, organism, freeze); else safef(buf, sizeof buf, "Configure Tracks on %s %s: %s %s (%s)", organization, browserName, organism, freeze, database); webNewSection(buf); hPrintf("Tracks: "); if(isSearchTracksSupported(database,cart)) { cgiMakeButtonWithMsg(TRACK_SEARCH, TRACK_SEARCH_BUTTON,TRACK_SEARCH_HINT); hPrintf(" "); } cgiMakeButtonWithMsg(configHideAll, "hide all","Hide all tracks in this genome assembly"); hPrintf(" "); cgiMakeButtonWithMsg(configShowAll, "show all","Show all tracks in this genome assembly"); hPrintf(" "); cgiMakeButtonWithMsg(configDefaultAll, "default","Display only default tracks"); hPrintf(" Groups: "); hButtonWithOnClick("hgt.collapseGroups", "collapse all", "Collapse all track groups", "return setAllTrackGroupVisibility(false)"); hPrintf(" "); hButtonWithOnClick("hgt.expandGroups", "expand all", "Expand all track groups", "return setAllTrackGroupVisibility(true)"); hPrintf("<P STYLE=\"margin-top:5;\">Control track and group visibility more selectively below.<P>"); trackConfig(trackList, groupList, groupTarget, vis); dyStringFree(&title); freez(&groupTarget); webEndSectionTables(); hPrintf("</FORM>"); }
void integerCellPrint(struct column *col, struct subjInfo *si, struct sqlConnection *conn) /* Print value including favorite hyperlink in debug column. */ { boolean special; special = FALSE; char *s = col->cellVal(col, si, conn); hPrintf("<TD align=right>"); if (sameWord(col->name, "cd4Count")) { if (sameWord(s, "-1") || sameWord(s, "0")) { printf("N/A"); special = TRUE; } } if (sameWord(col->name, "hivQuan")) { if (sameWord(s, "-1")) { printf("N/A"); special = TRUE; } } if (sameWord(col->name, "DAEI")) { if (sameWord(s, "-1")) { printf("N/A"); special = TRUE; } } if (sameWord(col->name, "esdi")) { if (sameWord(s, "-1")) { printf("N/A"); special = TRUE; } } if (sameWord(col->name, "hivQuan")) { if (sameWord(s, "1000000")) { printf("> 1000000"); special = TRUE; } } if (sameWord(col->name, "hivQuan")) { if (sameWord(s, "200")) { printf("< 400"); special = TRUE; } } if (!special) { hPrintf("%s", s); } freeMem(s); }
static void trackConfig(struct track *trackList, struct group *groupList, char *groupTarget, int changeVis) /* Put up track configurations. If groupTarget is * NULL then set visibility for tracks in all groups. Otherwise, * just set it for the given group. If vis is -2, then visibility is * unchanged. If -1 then set visibility to default, otherwise it should * be tvHide, tvDense, etc. */ { #ifdef PRIORITY_CHANGES_IN_CONFIG_UI char pname[512]; char gname[512]; #endif///def PRIORITY_CHANGES_IN_CONFIG_UI struct group *group; boolean showedRuler = FALSE; setRulerMode(); changeTrackVis(groupList, groupTarget, changeVis); /* Set up ruler mode according to changeVis. */ #ifdef BOB_DOESNT_LIKE if (changeVis != -2) { if (groupTarget == NULL || (groupList != NULL && sameString(groupTarget, groupList->name))) { if (changeVis == -1) rulerMode = tvFull; else rulerMode = changeVis; } } #endif /* BOB_DOESNT_LIKE */ jsInit(); cgiMakeHiddenVar(configGroupTarget, "none"); boolean isFirstNotCtGroup = TRUE; for (group = groupList; group != NULL; group = group->next) { struct trackRef *tr; if (group->trackList == NULL) continue; /* check if group section should be displayed */ char *otherState; char *indicator; char *indicatorImg; boolean isOpen = !isCollapsedGroup(group); collapseGroupGoodies(isOpen, FALSE, &indicatorImg, &indicator, &otherState); hTableStart(); hPrintf("<TR NOWRAP>"); hPrintf("<TH NOWRAP align=\"left\" colspan=3 BGCOLOR=#536ED3>"); hPrintf("\n<A NAME='%sGroup'></A>",group->name); hPrintf("<input type=hidden name='%s' id='%s' value=%d>", collapseGroupVar(group->name),collapseGroupVar(group->name), (isOpen?0:1)); hPrintf("<A HREF='%s?%s&%s=%s#%sGroup' class='bigBlue'><IMG height=22 width=22 onclick=\"return toggleTrackGroupVisibility(this,'%s');\" id='%s_button' src='%s' alt='%s' class='bigBlue' title='%s this group'></A> ", hgTracksName(), cartSidUrlString(cart),collapseGroupVar(group->name), otherState, group->name, group->name, group->name, indicatorImg, indicator,isOpen?"Collapse":"Expand"); hPrintf("<B> %s</B> ", wrapWhiteFont(group->label)); hPrintf(" "); hPrintf("<INPUT TYPE=SUBMIT NAME=\"%s\" VALUE=\"%s\" " "onClick=\"document.mainForm.%s.value='%s'; %s\" title='Hide all tracks in this groups'>", configHideAll, "hide all", configGroupTarget, group->name, jsSetVerticalPosition("mainForm")); hPrintf(" "); hPrintf("<INPUT TYPE=SUBMIT NAME=\"%s\" VALUE=\"%s\" " "onClick=\"document.mainForm.%s.value='%s'; %s\" title='Show all tracks in this groups'>", configShowAll, "show all", configGroupTarget, group->name, jsSetVerticalPosition("mainForm")); hPrintf(" "); hPrintf("<INPUT TYPE=SUBMIT NAME=\"%s\" VALUE=\"%s\" " "onClick=\"document.mainForm.%s.value='%s'; %s\" title='Show default tracks in this group'>", configDefaultAll, "default", configGroupTarget, group->name, jsSetVerticalPosition("mainForm")); hPrintf(" "); /* do not want all the submit buttons named the same. It is * confusing to the javascript submit() function. */ char submitName[256]; safef(submitName, sizeof(submitName), "%sSubmit", group->name); cgiMakeButtonWithMsg(submitName, "submit","Submit your selections and view them in the browser"); #ifdef PRIORITY_CHANGES_IN_CONFIG_UI if (withPriorityOverride) { hPrintf(" "); hPrintf(" "); hPrintf(" "); hPrintf("%s", wrapWhiteFont("Group Order: ")); } #endif///def PRIORITY_CHANGES_IN_CONFIG_UI hPrintf("</TH>\n"); #ifdef PRIORITY_CHANGES_IN_CONFIG_UI if (withPriorityOverride) { hPrintf("<TH>\n"); safef(pname, sizeof(pname), "%s.priority",group->name); hDoubleVar(pname, (double)group->priority, 4); hPrintf("</TH>\n"); if (isOpen) hPrintf("<TH align=CENTER BGCOLOR=#536ED3><B> %s</B></TH> ", wrapWhiteFont("Group")); hPrintf("\n"); } #endif///def PRIORITY_CHANGES_IN_CONFIG_UI hPrintf("</TR>\n"); /* First non-CT group gets ruler. */ if (!showedRuler && isFirstNotCtGroup && differentString(group->name, "user")) { showedRuler = TRUE; hPrintf("<TR %sid='%s-0'>",(isOpen ? "" : "style='display: none'"), group->name); hPrintf("<TD>"); hPrintf("<A HREF=\"%s?%s=%u&c=%s&g=%s&hgTracksConfigPage=configure\">", hgTrackUiName(), cartSessionVarName(), cartSessionId(cart), chromName, RULER_TRACK_NAME); hPrintf("%s</A>", RULER_TRACK_LABEL); hPrintf("</TD>"); hPrintf("<TD>"); hTvDropDownClass("ruler", rulerMode, FALSE, rulerMode ? "normalText" : "hiddenText"); hPrintf("</TD>"); hPrintf("<TD>"); hPrintf("Chromosome position in bases. (Clicks here zoom in 3x)"); hPrintf("</TD>"); #ifdef PRIORITY_CHANGES_IN_CONFIG_UI if (withPriorityOverride) { hPrintf("<TD>"); hPrintf("</TD>"); hPrintf("<TD>"); hPrintf("</TD>"); } #endif///def PRIORITY_CHANGES_IN_CONFIG_UI hPrintf("</TR>\n"); } if (differentString(group->name, "user")) isFirstNotCtGroup = FALSE; /* Scan track list to determine which supertracks have visible member * tracks, and to insert a track in the list for the supertrack. * Sort tracks and supertracks together by priority */ groupTrackListAddSuper(cart, group); if (!withPriorityOverride) { /* sort hierarchically by priority, considering supertracks */ struct trackRef *refList = NULL, *ref; for (tr = group->trackList; tr != NULL; tr = tr->next) { struct track *track = tr->track; if (tdbIsSuperTrackChild(track->tdb)) /* ignore supertrack member tracks till supertrack is found */ continue; AllocVar(ref); ref->track = track; slAddTail(&refList, ref); if (tdbIsSuper(track->tdb)) { struct trackRef *tr2; for (tr2 = group->trackList; tr2 != NULL; tr2 = tr2->next) { char *parent = tr2->track->tdb->parentName; if (parent && sameString(parent, track->track)) { AllocVar(ref); ref->track = tr2->track; slAddTail(&refList, ref); } } } } group->trackList = refList; } /* Loop through this group and display */ int rowCount=1; for (tr = group->trackList; tr != NULL; tr = tr->next) { struct track *track = tr->track; struct trackDb *tdb = track->tdb; hPrintf("<TR %sid='%s-%d'>",(isOpen ? "" : "style='display: none'"),group->name, rowCount++); hPrintf("<TD NOWRAP>"); if (tdbIsSuperTrackChild(tdb)) /* indent members of a supertrack */ hPrintf(" "); // Print an icon before the title when one is defined hPrintPennantIcon(track->tdb); if (track->hasUi) hPrintf("<A %s%s%s HREF=\"%s?%s=%u&g=%s&hgTracksConfigPage=configure\">", tdb->parent ? "TITLE=\"Part of super track: " : "", tdb->parent ? tdb->parent->shortLabel : "", tdb->parent ? "...\"" : "", hgTrackUiName(), cartSessionVarName(), cartSessionId(cart), track->track); hPrintf(" %s", track->shortLabel); if (tdbIsSuper(track->tdb)) hPrintf("..."); if (track->hasUi) hPrintf("</A>"); hPrintf("</TD>"); hPrintf("<TD NOWRAP>"); if (tdbIsSuperTrackChild(tdb)) /* indent members of a supertrack */ hPrintf(" "); /* If track is not on this chrom print an informational message for the user. */ if (hTrackOnChrom(track->tdb, chromName)) { if (tdbIsSuper(track->tdb)) { /* supertrack dropdown is hide/show */ superTrackDropDown(cart, track->tdb, 1); } else { /* check for option of limiting visibility to one mode */ hTvDropDownClassVisOnly(track->track, track->visibility, track->canPack, (track->visibility == tvHide) ? "hiddenText" : "normalText", trackDbSetting(track->tdb, "onlyVisibility")); } } else hPrintf("[No data-%s]", chromName); hPrintf("</TD>"); hPrintf("<TD NOWRAP>"); hPrintf("%s", track->longLabel); hPrintf("</TD>"); #ifdef PRIORITY_CHANGES_IN_CONFIG_UI if (withPriorityOverride) { hPrintf("<TD>"); safef(pname, sizeof(pname), "%s.priority",track->track); hDoubleVar(pname, (double)track->priority, 4); hPrintf("</TD>"); hPrintf("<TD>\n"); /* suppress group pull-down for supertrack members */ if (tdbIsSuperTrackChild(track->tdb)) hPrintf(" "); else { safef(gname, sizeof(gname), "%s.group",track->track); printGroupListHtml(gname, groupList, track->groupName); } hPrintf("</TD>"); } #endif///def PRIORITY_CHANGES_IN_CONFIG_UI hPrintf("</TR>\n"); } hTableEnd(); hPrintf("<BR>"); } }
void configPageSetTrackVis(int vis) /* Do config page after setting track visibility. If vis is -2, then visibility * is unchanged. If -1 then set visibility to default, otherwise it should * be tvHide, tvDense, etc. */ { char *groupTarget; struct track *trackList; struct track *ideoTrack; struct group *groupList; configInitTrackList(vis, &groupTarget, &trackList, &ideoTrack, &groupList); struct dyString *title = dyStringNew(0); dyStringPrintf(title, "Configure Image"); hPrintf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=%s>\n", hgTracksName(), cartUsualString(cart, "formMethod", "POST")); webStartWrapperDetailedNoArgs(cart, database, "", title->string, FALSE, FALSE, FALSE, FALSE); cartSaveSession(cart); hPrintf("<INPUT TYPE=HIDDEN NAME=\"hgTracksConfigPage\" VALUE=\"\">"); /* do not want all the submit buttons named the same thing, this one is: */ cgiMakeButton("topSubmit", "submit"); // 3 column table hPrintf("<TABLE style=\"border:0px; \">\n"); hPrintf("<TR><TD>image width:"); hPrintf("<TD style=\"text-align: right\">"); hIntVar("pix", tl.picWidth, 4); hPrintf("<TD>pixels</TR>"); hPrintf("<TR><TD>label area width:"); hPrintf("<TD style=\"text-align: right\">"); hIntVar("hgt.labelWidth", leftLabelWidthChars, 2); hPrintf("<TD>characters<TD></TR>"); hPrintf("<TR><TD>text size:"); hPrintf("<TD style=\"text-align: right\">"); textSizeDropDown(); hPrintf("</TD>"); if (trackLayoutInclFontExtras()) { hPrintf("<TD>"); char *defaultStyle = cartUsualString(cart, "fontType", "medium"); cartMakeRadioButton(cart, "fontType", "medium", defaultStyle); hPrintf(" medium "); cartMakeRadioButton(cart, "fontType", "fixed", defaultStyle); hPrintf(" fixed "); cartMakeRadioButton(cart, "fontType", "bold", defaultStyle); hPrintf(" bold "); hPrintf(" "); hPrintf("</TD>"); } hPrintf("</TR>"); themeDropDown(cart); hTableStart(); if (ideoTrack != NULL) { hPrintf("<TR><TD>"); hCheckBox("ideogram", cartUsualBoolean(cart, "ideogram", TRUE)); hPrintf("</TD><TD>"); hPrintf("Display chromosome ideogram above main graphic"); hPrintf("</TD></TR>\n"); } hPrintf("<TR><TD>"); hCheckBox("guidelines", cartUsualBoolean(cart, "guidelines", TRUE)); hPrintf("</TD><TD>"); hPrintf("Show light blue vertical guidelines, or light red vertical window separators in multi-region view"); hPrintf("</TD></TR>\n"); hPrintf("<TR><TD>"); hCheckBox("leftLabels", cartUsualBoolean(cart, "leftLabels", TRUE)); hPrintf("</TD><TD>"); hPrintf("Display labels to the left of items in tracks"); hPrintf("</TD></TR>\n"); hPrintf("<TR><TD>"); hCheckBox("centerLabels", cartUsualBoolean(cart, "centerLabels", TRUE)); hPrintf("</TD><TD>"); hPrintf("Display description above each track"); hPrintf("</TD></TR>\n"); hPrintf("<TR><TD>"); hCheckBox("trackControlsOnMain", cartUsualBoolean(cart, "trackControlsOnMain", TRUE)); hPrintf("</TD><TD>"); hPrintf("Show track controls under main graphic"); hPrintf("</TD></TR>\n"); hPrintf("<TR><TD>"); hCheckBox("nextItemArrows", cartUsualBoolean(cart, "nextItemArrows", FALSE)); hPrintf("</TD><TD>"); hPrintf("Next/previous item navigation"); hPrintf("</TD></TR>\n"); hPrintf("<TR><TD>"); hCheckBox("nextExonArrows", cartUsualBoolean(cart, "nextExonArrows", TRUE)); hPrintf("</TD><TD>"); hPrintf("Next/previous exon navigation"); hPrintf("</TD></TR>\n"); hPrintf("<TR><TD>"); hCheckBox("exonNumbers", cartUsualBoolean(cart, "exonNumbers", TRUE)); hPrintf("</TD><TD>"); hPrintf("Show exon numbers"); hPrintf("</TD></TR>\n"); hPrintf("<TR><TD>"); hCheckBox("enableHighlightingDialog", cartUsualBoolean(cart, "enableHighlightingDialog", TRUE)); hPrintf("</TD><TD>"); hPrintf("Enable highlight with drag-and-select " "(if unchecked, drag-and-select always zooms to selection)"); hPrintf("</TD></TR>\n"); hTableEnd(); cgiDown(0.9); char buf[256]; char *freeze = hFreezeFromDb(database); if (freeze == NULL) safef(buf, sizeof buf, "Configure Tracks on %s %s: %s", organization, browserName, trackHubSkipHubName(organism)); else if (stringIn(database, freeze)) safef(buf, sizeof buf, "Configure Tracks on %s %s: %s %s", organization, browserName, trackHubSkipHubName(organism), freeze); else safef(buf, sizeof buf, "Configure Tracks on %s %s: %s %s (%s)", organization, browserName, trackHubSkipHubName(organism), freeze, trackHubSkipHubName(database)); webNewSection("%s",buf); hPrintf("Tracks: "); if (isSearchTracksSupported(database,cart)) { cgiMakeButtonWithMsg(TRACK_SEARCH, TRACK_SEARCH_BUTTON,TRACK_SEARCH_HINT); hPrintf(" "); } cgiMakeButtonWithMsg(configHideAll, "hide all","Hide all tracks in this genome assembly"); hPrintf(" "); cgiMakeButtonWithMsg(configShowAll, "show all","Show all tracks in this genome assembly"); hPrintf(" "); cgiMakeButtonWithMsg(configDefaultAll, "default","Display only default tracks"); hPrintf(" Groups: "); hButtonWithOnClick("hgt.collapseGroups", "collapse all", "Collapse all track groups", "return vis.expandAllGroups(false)"); hPrintf(" "); hButtonWithOnClick("hgt.expandGroups", "expand all", "Expand all track groups", "return vis.expandAllGroups(true)"); hPrintf("<div style='margin-top:.2em; margin-bottom:.9em;'>Control track and group visibility " "more selectively below.</div>"); trackConfig(trackList, groupList, groupTarget, vis); dyStringFree(&title); freez(&groupTarget); webEndSectionTables(); hPrintf("</FORM>"); }
void doIntersectMore(struct sqlConnection *conn) /* Continue working in intersect page. */ { struct trackDb *iTrack; char *name = curTableLabel(); char *iName, *iTable; char *onChange = onChangeEither(); char *op, *setting; boolean wigOptions = (isWiggle(database, curTable) || isBedGraph(curTable)); // Note - bigWig is purposely left out of wigOptions. It supports more intersection options // than wig does. struct hTableInfo *hti1 = maybeGetHti(database, curTable, conn), *hti2 = NULL; htmlOpen("Intersect with %s", name); hPrintf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=GET>\n", getScriptName()); cartSaveSession(cart); hPrintf("<TABLE BORDER=0>\n"); /* Print group and track line. */ hPrintf("Select a group, track and table to intersect with:\n"); iTrack = showGroupTrackRow(hgtaNextIntersectGroup, onChange, hgtaNextIntersectTrack, onChange, conn); iName = iTrack->shortLabel; hPrintf("<TR><TD>\n"); iTable = showTableField(iTrack, hgtaNextIntersectTable, FALSE); hti2 = maybeGetHti(database, iTable, conn); hPrintf("</TD></TR>\n"); hPrintf("</TABLE>\n"); if (!wigOptions) { if (hti1 && hti1->hasBlocks) hPrintf("<BR>Note: %s has gene/alignment structure. " "Only the exons/blocks will be considered.\n", name); if (hti2 && hti2->hasBlocks) hPrintf("<BR>Note: %s has gene/alignment structure. " "Only the bases covered by its exons/blocks will be " "considered.\n", iName); hPrintf("<H4>Intersect %s items with bases covered by %s:</H4>\n", name, iName); hPrintf("These combinations will maintain the names and " "gene/alignment structure (if any) of %s: <P>\n", name); } else hPrintf("<P>\n"); op = cartUsualString(cart, hgtaNextIntersectOp, "any"); jsTrackingVar("op", op); makeOpButton("any", op); printf("All %s records that have any overlap with %s <BR>\n", name, iName); makeOpButton("none", op); printf("All %s records that have no overlap with %s <BR>\n", name, iName); if (!wigOptions) { makeOpButton("more", op); printf("All %s records that have at least ", name); setting = cartCgiUsualString(cart, hgtaNextMoreThreshold, "80"); cgiMakeTextVar(hgtaNextMoreThreshold, setting, 3); printf(" %% overlap with %s <BR>\n", iName); makeOpButton("less", op); printf("All %s records that have at most ", name); setting = cartCgiUsualString(cart, hgtaNextLessThreshold, "80"); cgiMakeTextVar(hgtaNextLessThreshold, setting, 3); printf(" %% overlap with %s <P>\n", iName); } else { /* keep javaScript onClick happy */ hPrintf("<input TYPE=HIDDEN NAME=\"hgta_nextMoreThreshold\" VALUE=80>\n"); hPrintf("<input TYPE=HIDDEN NAME=\"hgta_nextLessThreshold\" VALUE=80>\n"); hPrintf(" <P>\n"); } if (!wigOptions) { boolean bigWig = isBigWigTable(curTable); hPrintf("<H4>Intersect bases covered by %s and/or %s:</H4>\n", name, iName); if (!bigWig) hPrintf("These combinations will discard the names and " "gene/alignment structure (if any) of %s and produce a simple " "list of position ranges.<P>\n", name); makeOpButton("and", op); printf("Base-pair-wise intersection (AND) of %s and %s <BR>\n", name, iName); makeOpButton("or", op); printf("Base-pair-wise union (OR) of %s and %s <P>\n", name, iName); hPrintf("Check the following boxes to complement one or both tables. " "To complement a table means to include a base pair in the " "intersection/union if it is <I>not</I> included in the table." "<P>\n"); if (!bigWig) { jsMakeTrackingCheckBox(cart, hgtaNextInvertTable, "invertTable", FALSE); printf("Complement %s before base-pair-wise intersection/union <BR>\n", name); } jsMakeTrackingCheckBox(cart, hgtaNextInvertTable2, "invertTable2", FALSE); printf("Complement %s before base-pair-wise intersection/union <P>\n", iName); } else { /* keep javaScript onClick happy */ jsTrackingVar("op", op); hPrintf("<SCRIPT>\n"); hPrintf("var invertTable=0;\n"); hPrintf("var invertTable2=0;\n"); hPrintf("</SCRIPT>\n"); hPrintf("(data track %s is not composed of gene records. Specialized intersection operations are not available.)<P>\n", name); } cgiMakeButton(hgtaDoIntersectSubmit, "submit"); hPrintf(" "); cgiMakeButton(hgtaDoMainPage, "cancel"); hPrintf("</FORM>\n"); /* Hidden form - for benefit of javascript. */ { static char *saveVars[32]; int varCount = ArraySize(nextVars); memcpy(saveVars, nextVars, varCount * sizeof(saveVars[0])); saveVars[varCount] = hgtaDoIntersectMore; jsCreateHiddenForm(cart, getScriptName(), saveVars, varCount+1); } htmlClose(); }
static void trackConfig(struct track *trackList, struct group *groupList, char *groupTarget, int changeVis) /* Put up track configurations. If groupTarget is * NULL then set visibility for tracks in all groups. Otherwise, * just set it for the given group. If vis is -2, then visibility is * unchanged. If -1 then set visibility to default, otherwise it should * be tvHide, tvDense, etc. */ { struct group *group; boolean showedRuler = FALSE; setRulerMode(); changeTrackVis(groupList, groupTarget, changeVis); /* Set up ruler mode according to changeVis. */ #ifdef BOB_DOESNT_LIKE if (changeVis != -2) { if (groupTarget == NULL || (groupList != NULL && sameString(groupTarget, groupList->name))) { if (changeVis == -1) rulerMode = tvFull; else rulerMode = changeVis; } } #endif /* BOB_DOESNT_LIKE */ jsInit(); cgiMakeHiddenVar(configGroupTarget, "none"); // Now all groups are in a single table, divided by an empty borderless row hPrintf("<TABLE BORDER='0' CELLSPACING='0' class='groupLists'>\n"); for (group = groupList; group != NULL; group = group->next) { struct trackRef *tr; if (group->trackList == NULL) continue; /* check if group section should be displayed */ char *otherState; char *indicator; char *indicatorImg; boolean isOpen = !isCollapsedGroup(group); collapseGroupGoodies(isOpen, FALSE, &indicatorImg, &indicator, &otherState); hPrintf("<TR NOWRAP class='blueToggleBar'>"); hPrintf("<TH NOWRAP align='left' colspan=3>"); hPrintf("<table style='width:100%%;'><tr class='noData'><td style='text-align:left;'>"); hPrintf("\n<A NAME='%sGroup'></A>",group->name); hPrintf("<input type=hidden name='%s' id='%s' value=%d>", collapseGroupVar(group->name),collapseGroupVar(group->name), (isOpen?0:1)); char idText[256]; safef(idText, sizeof idText, "%s_button", group->name); hPrintf("<IMG class='toggleButton' " "id='%s' src='%s' alt='%s' title='%s this group'> ", idText, indicatorImg, indicator,isOpen?"Collapse":"Expand"); // TODO XSS filter group->name jsOnEventByIdF("click", idText, "return vis.toggleForGroup(this,'%s');", group->name); hPrintf("<B> %s</B> ", group->label); hPrintf(" "); hPrintf("</td><td style='text-align:right;'>\n"); safef(idText, sizeof idText, "%s_hideAllBut", group->name); hPrintf("<INPUT TYPE=SUBMIT NAME=\"%s\" id='%s' VALUE=\"%s\" " "title='Hide all tracks in this groups'>", configHideAll, idText, "hide all"); // TODO XSS filter configGroupTarget char jsText[256]; // used several times safef(jsText, sizeof jsText, "document.mainForm.%s.value='%s'; %s", configGroupTarget, group->name, jsSetVerticalPosition("mainForm")); jsOnEventById("click", idText, jsText); hPrintf(" "); safef(idText, sizeof idText, "%s_showAllBut", group->name); hPrintf("<INPUT TYPE=SUBMIT NAME=\"%s\" id='%s' VALUE=\"%s\" " "title='Show all tracks in this groups'>", configShowAll, idText, "show all"); jsOnEventById("click", idText, jsText); hPrintf(" "); safef(idText, sizeof idText, "%s_defaultBut", group->name); hPrintf("<INPUT TYPE=SUBMIT NAME=\"%s\" id='%s' VALUE=\"%s\" " "title='Show default tracks in this group'>", configDefaultAll, idText, "default"); jsOnEventById("click", idText, jsText); hPrintf(" "); /* do not want all the submit buttons named the same. It is * confusing to the javascript submit() function. */ char submitName[256]; safef(submitName, sizeof(submitName), "%sSubmit", group->name); cgiMakeButtonWithMsg(submitName, "submit","Submit your selections and view them in the browser"); hPrintf("</td></tr></table>\n"); hPrintf("</TH></TR>\n"); /* First non-CT, non-hub group gets ruler. */ if (!showedRuler && !isHubTrack(group->name) && differentString(group->name, "user")) { showedRuler = TRUE; hPrintf("<TR %sid='%s-0'>",(isOpen ? "" : "style='display: none'"), group->name); hPrintf("<TD>"); hPrintf("<A HREF=\"%s?%s=%s&c=%s&g=%s&hgTracksConfigPage=configure\">", hgTrackUiName(), cartSessionVarName(), cartSessionId(cart), chromName, RULER_TRACK_NAME); hPrintf("%s</A>", RULER_TRACK_LABEL); hPrintf("</TD><TD>"); hTvDropDownClass("ruler", rulerMode, FALSE, rulerMode ? "normalText" : "hiddenText"); hPrintf("</TD><TD>"); hPrintf("Chromosome position in bases. (Clicks here zoom in 3x)"); hPrintf("</TD></TR>\n"); } /* Scan track list to determine which supertracks have visible member * tracks, and to insert a track in the list for the supertrack. * Sort tracks and supertracks together by priority */ makeGlobalTrackHash(trackList); groupTrackListAddSuper(cart, group); if (!withPriorityOverride) { /* sort hierarchically by priority, considering supertracks */ struct trackRef *refList = NULL, *ref; for (tr = group->trackList; tr != NULL; tr = tr->next) { struct track *track = tr->track; if (tdbIsSuperTrackChild(track->tdb)) /* ignore supertrack member tracks till supertrack is found */ continue; AllocVar(ref); ref->track = track; slAddTail(&refList, ref); if (tdbIsSuper(track->tdb)) { struct slRef *child = track->tdb->children; for (; child != NULL; child=child->next) { struct trackDb *childTdb = child->val; struct track *childTrack = hashFindVal(trackHash, childTdb->track); // Try adding downloadsOnly track if (childTrack == NULL && tdbIsDownloadsOnly(childTdb)) { AllocVar(childTrack); // Fake a track! childTrack->tdb = childTdb; childTrack->hasUi = FALSE; } if (childTrack != NULL) { AllocVar(ref); ref->track = childTrack; slAddTail(&refList, ref); } } } } group->trackList = refList; } /* Loop through this group and display */ int rowCount=1; for (tr = group->trackList; tr != NULL; tr = tr->next) { struct track *track = tr->track; struct trackDb *tdb = track->tdb; hPrintf("<TR %sid='%s-%d'>",(isOpen ? "" : "style='display: none;'"), group->name, rowCount++); hPrintf("<TD NOWRAP>"); if (tdbIsSuperTrackChild(tdb)) /* indent members of a supertrack */ hPrintf(" "); // Print an icon before the title when one is defined hPrintPennantIcon(tdb); if (track->hasUi) hPrintf("<A TITLE='%s%s...' HREF='%s?%s=%s&g=%s&hgTracksConfigPage=configure'>", tdb->parent ? "Part of super track: " : "Configure ", tdb->parent ? tdb->parent->shortLabel : tdb->shortLabel, hTrackUiForTrack(tdb->track), cartSessionVarName(), cartSessionId(cart), track->track); hPrintf(" %s", tdb->shortLabel); if (tdbIsSuper(tdb)) hPrintf("..."); if (track->hasUi) hPrintf("</A>"); hPrintf("</TD><TD NOWRAP>"); if (tdbIsSuperTrackChild(tdb)) /* indent members of a supertrack */ hPrintf(" "); /* If track is not on this chrom print an informational message for the user. */ if (tdbIsDownloadsOnly(tdb)) // No vis display for downloadsOnly hPrintf("<A TITLE='Downloadable files...' HREF='%s?%s=%s&g=%s'>Downloads</A>", hgFileUiName(),cartSessionVarName(), cartSessionId(cart), tdb->track); else if (hTrackOnChrom(track->tdb, chromName)) { if (tdbIsSuper(track->tdb)) { /* supertrack dropdown is hide/show */ superTrackDropDown(cart, track->tdb, 1); } else { /* check for option of limiting visibility to one mode */ hTvDropDownClassVisOnly(track->track, track->visibility, rTdbTreeCanPack(track->tdb), (track->visibility == tvHide) ? "hiddenText" : "normalText", trackDbSetting(track->tdb, "onlyVisibility")); } } else hPrintf("[No data-%s]", chromName); hPrintf("</TD><TD NOWRAP>"); hPrintf("%s", tdb->longLabel); hPrintf("</TD></TR>\n"); } hPrintf("<tr class='noData'><td colspan=3>"); cgiDown(0.9); hPrintf("</td></tr>\n"); } hPrintf("</TABLE>\n"); }
void bigTable(struct sqlConnection *conn, struct column *colList, struct subjInfo *siList) /* Put up great big table. */ { struct column *col; struct subjInfo *si; if (siList == NULL) { if (gotAdvFilter()) { warn("No subjects passed filter."); } return; } hPrintf("<CENTER>"); hPrintf("<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=1 COLS=%d BGCOLOR=\"#"HG_COL_INSIDE"\">\n", totalHtmlColumns(colList)); /* Print label row. */ hPrintf("<TR BGCOLOR=\"#"HG_COL_HEADER"\">"); for (col = colList; col != NULL; col = col->next) { if (col->on) { col->labelPrint(col); } } hPrintf("</TR>\n"); /* Print other rows. */ hPrintf("<!-- Start Rows -->"); for (si = siList; si != NULL; si = si->next) { hPrintf("<TR>"); for (col = colList; col != NULL; col = col->next) { if (col->on) { if (col->cellPrint == NULL) hPrintf("<TD></TD>"); else col->cellPrint(col,si,conn); } } hPrintf("</TR><!-- Row -->\n"); if (ferror(stdout)) errAbort("Write error to stdout"); } hPrintf("<!-- End Rows -->"); hPrintf("</TABLE>\n"); hPrintf("<BR>Displayed %d out of %d subjects passing filter.", slCount(siList), passedFilterCount); hPrintf("</CENTER>"); }
void doSummaryStatsBed(struct sqlConnection *conn) /* Put up page showing summary stats for track that is in database * or that is bed-format custom. */ { struct bed *bedList = NULL; struct region *regionList = getRegions(), *region; char *regionName = getRegionName(); long long regionSize = 0, gapTotal = 0, realSize = 0; long startTime, midTime, endTime; long loadTime = 0, calcTime = 0, freeTime = 0; struct covStats *itemCovList = NULL, *blockCovList = NULL, *cov; int itemCount = 0; struct hTableInfo *hti = getHti(database, curTable, conn); int minScore = BIGNUM, maxScore = -BIGNUM; long long sumScores = 0; boolean hasBlocks = hti->hasBlocks; boolean hasScore = (hti->scoreField[0] != 0); int fieldCount; htmlOpen("%s (%s) Summary Statistics", curTableLabel(), curTable); for (region = regionList; region != NULL; region = region->next) { struct lm *lm = lmInit(64*1024); startTime = clock1000(); bedList = cookedBedList(conn, curTable, region, lm, &fieldCount); if (fieldCount < 12) hasBlocks = FALSE; if (fieldCount < 5) hasScore = FALSE; midTime = clock1000(); loadTime += midTime - startTime; if (bedList != NULL) { itemCount += slCount(bedList); regionSize += region->end - region->start; cov = calcSpanOverRegion(region, bedList); slAddHead(&itemCovList, cov); if (hasBlocks) { cov = calcBlocksOverRegion(region, bedList); slAddHead(&blockCovList, cov); } if (hti->scoreField[0] != 0) { struct bed *bed; for (bed = bedList; bed != NULL; bed = bed->next) { int score = bed->score; if (score < minScore) minScore = score; if (score > maxScore) maxScore = score; sumScores += score; } } } endTime = clock1000(); calcTime += endTime - midTime; lmCleanup(&lm); bedList = NULL; freeTime += clock1000() - endTime; } regionSize = basesInRegion(regionList, 0); gapTotal = gapsInRegion(conn, regionList, 0); realSize = regionSize - gapTotal; hTableStart(); startTime = clock1000(); numberStatRow("item count", itemCount); if (itemCount > 0) { cov = covStatsSum(itemCovList); percentStatRow("item bases", cov->basesCovered, realSize); percentStatRow("item total", cov->sumBases, realSize); numberStatRow("smallest item", cov->minBases); numberStatRow("average item", round((double)cov->sumBases/cov->itemCount)); numberStatRow("biggest item", cov->maxBases); } if (hasBlocks && itemCount > 0) { cov = covStatsSum(blockCovList); hPrintf("<TR><TD>block count</TD><TD ALIGN=RIGHT>"); printLongWithCommas(stdout, cov->itemCount); hPrintf("</TD></TR>\n"); percentStatRow("block bases", cov->basesCovered, realSize); percentStatRow("block total", cov->sumBases, realSize); numberStatRow("smallest block", cov->minBases); numberStatRow("average block", round((double)cov->sumBases/cov->itemCount)); numberStatRow("biggest block", cov->maxBases); } if (hasScore != 0 && itemCount > 0 && sumScores != 0) { numberStatRow("smallest score", minScore); numberStatRow("average score", round((double)sumScores/itemCount)); numberStatRow("biggest score", maxScore); } hTableEnd(); /* Show region and time stats part of stats page. */ webNewSection("Region and Timing Statistics"); hTableStart(); stringStatRow("region", regionName); numberStatRow("bases in region", regionSize); numberStatRow("bases in gaps", gapTotal); floatStatRow("load time", 0.001*loadTime); floatStatRow("calculation time", 0.001*calcTime); floatStatRow("free memory time", 0.001*freeTime); stringStatRow("filter", (anyFilter() ? "on" : "off")); stringStatRow("intersection", (anyIntersection() ? "on" : "off")); hTableEnd(); covStatsFreeList(&itemCovList); covStatsFreeList(&blockCovList); htmlClose(); }
int main(int argc, char *argv[]) /* Process command line. */ { pushCarefulMemHandler(100000000); cgiSpoof(&argc, argv); htmlSetStyle(htmlStyleUndecoratedLink); htmlSetBgColor(HG_CL_OUTSIDE); oldCart = hashNew(10); cart = cartAndCookie(hUserCookie(), excludeVars, oldCart); getDbAndGenome(cart, &database, &genome, oldCart); //hSetDb(database); conn = hAllocConn(database); database = strdup("h1n1"); /* Get sortOn. Revert to default by subject Id. */ orderOn = cartUsualString(cart, orderVarName, "+subjId"); displayCountString = cartUsualString(cart, countVarName, "50"); if (sameString(displayCountString, "all")) displayCount = BIGNUM; else displayCount = atoi(displayCountString); colList = getColumns(conn); if (cgiVarExists("submit_filter")) { struct dyString *head = dyStringNew(1024); boolean redir = cgiVarExists(redirectName); struct subjInfo *subjList = NULL; struct column *ordList = colList; struct column *ord = curOrder(ordList); subjList = getOrderedList(ord, colList, conn, BIGNUM); saveSubjList(subjList); if ((!subjList || redir)) { if (subjList && redir) { dyStringPrintf(head, "<META HTTP-EQUIV=\"REFRESH\" CONTENT=\"0;URL=/cgi-bin/%s\">" "<META HTTP-EQUIV=\"Pragma\" CONTENT=\"no-cache\">" "<META HTTP-EQUIV=\"Expires\" CONTENT=\"-1\">" , cgiString(redirectName)); cartRemove(cart, redirectName); } htmStartWithHead(stdout, head->string, "GISAID Table View"); if (!subjList) /* if everything has been filtered out, we'll have to go back */ { hPrintf("No subject(s) found with the filtering conditions specified.<br>"); hPrintf("Click <a href=\"gisaidTable?gisaidTable.do.advFilter=filter+%%28now+on%%29\">here</a> " "to return to Select Subjects.<br>"); } cartCheckout(&cart); htmlEnd(); hFreeConn(&conn); return 0; } } htmStart(stdout, "GISAID Table View"); cartWarnCatcher(doMiddle, cart, htmlVaWarn); cartCheckout(&cart); htmlEnd(); hFreeConn(&conn); return 0; }
static void configTable(struct column *colList, struct sqlConnection *conn) /* Write out configuration table */ { struct column *col; char varName[128]; boolean isVis; hPrintf("<center>"); hPrintf("<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=1 BGCOLOR=\"#"HG_COL_INSIDE"\">\n"); /* Write out first row - labels. */ hPrintf("<TR BGCOLOR=\"#"HG_COL_HEADER"\">"); hPrintf("<TH ALIGN=left>Name</TH>"); hPrintf("<TH ALIGN=left>On</TH>"); //hPrintf("<TH ALIGN=left>Position</TH>"); hPrintf("<TH ALIGN=left>Description</TH>"); //hPrintf("<TH ALIGN=left>Configuration</TH>"); /* Print out configuration controls. */ hPrintf("</TR>"); /* Write out other rows. */ for (col = colList; col != NULL; col = col->next) { hPrintf("<TR>"); /* Do small label. */ hPrintf("<TD>%s</TD>", col->shortLabel); /* Do on/off dropdown. */ hPrintf("<TD>"); safef(varName, sizeof(varName), "%s%s.vis", colConfigPrefix, col->name); isVis = cartUsualBoolean(cart, varName, col->on); cgiMakeCheckBox(varName, isVis); hPrintf("</TD>"); ///* Do left/right button */ //hPrintf("<TD ALIGN=CENTER>"); //safef(varName, sizeof(varName), "gisaidTable.do.up.%s", col->name); //if (col != colList) // { // hPrintf("<INPUT NAME=\"%s\" TYPE=\"IMAGE\" VALUE=\"up\" ", varName); // hPrintf("SRC=\"../images/up.gif\">"); // } //safef(varName, sizeof(varName), "gisaidTable.do.down.%s", col->name); //if (col->next != NULL) // { // hPrintf("<INPUT NAME=\"%s\" TYPE=\"IMAGE\" VALUE=\"down\" ", varName); // hPrintf("SRC=\"../images/down.gif\">"); // } //hPrintf("</TD>"); /* Do long label. */ hPrintf("<TD>%s</TD>", col->longLabel); ///* Do configuration controls. */ //if (col->configControls != NULL) // col->configControls(col); //else // hPrintf("<TD>n/a</TD>"); hPrintf("</TR>\n"); } hPrintf("</TABLE>\n"); hPrintf("</center>"); }
void doGetText(struct sqlConnection *conn, struct column *colList, struct subjInfo *subjList) /* Put up great big table. */ { struct subjInfo *si; struct column *col; boolean first = TRUE; char *chp, *chp9; if (subjList == NULL) { hPrintf("empty table"); return; } hPrintf("<TT><PRE>"); /* Print labels. */ hPrintf("#"); for (col = colList; col != NULL; col = col->next) { if (col->on) { if (first) first = FALSE; else hPrintf("\t"); hPrintf("%s", col->shortLabel); } } hPrintf("\n"); for (si = subjList; si != NULL; si = si->next) { first = TRUE; for (col = colList; col != NULL; col = col->next) { if (col->on) { boolean special; char *val = col->cellVal(col, si, conn); if (first) first = FALSE; else hPrintf("\t"); if (val == NULL) hPrintf("n/a"); else { special = FALSE; if (sameWord(col->name, "cd4Count")) { if (sameWord(val, "-1") || sameWord(val, "0")) { hPrintf("N/A"); special = TRUE; } } if (sameWord(col->name, "hivQuan")) { if (sameWord(val, "-1")) { hPrintf("N/A"); special = TRUE; } } if (sameWord(col->name, "DAEI")) { if (sameWord(val, "-1")) { hPrintf("N/A"); special = TRUE; } } if (sameWord(col->name, "esdi")) { if (sameWord(val, "-1")) { hPrintf("N/A"); special = TRUE; } } if (sameWord(col->name, "hivQuan")) { if (sameWord(val, "1000000")) { hPrintf("> 1000000"); special = TRUE; } } if (sameWord(col->name, "hivQuan")) { if (sameWord(val, "200")) { hPrintf("< 400"); special = TRUE; } } if ((sameWord(col->name, "dnaSeqIds")) || (sameWord(col->name, "aaSeqIds"))) { chp = val; chp = strstr(chp, "#35;"); while (chp != NULL) { chp = chp +strlen("#35;"); chp9 = strstr(chp, " "); *chp9 = '\0'; hPrintf("%s ", chp); chp9++; chp = strstr(chp9, "#35;"); } special = TRUE; } if (!special) { hPrintf("%s", val); } } freez(&val); } } hPrintf("\n"); } hPrintf("</PRE></TT>"); }
static void domainsPrint(struct section *section, struct sqlConnection *conn, char *geneId) /* Print out protein domains. */ { char *db = sqlGetDatabase(conn); struct slName *el, *list; list = spExtDbAcc1List(spConn, swissProtAcc, "Interpro"); if (list != NULL) { char query[256], **row, **row2; struct sqlResult *sr, *sr2; hPrintf("<B>InterPro Domains: </B> "); hPrintf("<A HREF=\"http://www.ebi.ac.uk/interpro/protein/%s\" TARGET=_blank>", swissProtAcc); hPrintf("Graphical view of domain structure</A><BR>"); sqlSafef(query, sizeof(query), "select extAcc1,extAcc2 from extDbRef,extDb" " where extDbRef.acc = '%s'" " and extDb.val = 'Interpro' and extDb.id = extDbRef.extDb" , swissProtAcc); sr = sqlGetResult(spConn, query); while ((row = sqlNextRow(sr)) != NULL) { //hPrintf("<A HREF=\"http://www.ebi.ac.uk/interpro/entry/%s\" TARGET=_blank>", row[0]); //hPrintf("%s</A> - %s<BR>\n", row[0], row[1]); char interPro[256]; char *pdb = hPdbFromGdb(db); safef(interPro, 128, "%s.interProXref", pdb); if (hTableExists(db, interPro)) { sqlSafef(query, sizeof(query), "select description from %s where accession = '%s' and interProId = '%s'", interPro, swissProtAcc, row[0]); sr2 = sqlGetResult(conn, query); if ((row2 = sqlNextRow(sr2)) != NULL) { hPrintf("<A HREF=\"http://www.ebi.ac.uk/interpro/entry/%s\" TARGET=_blank>", row[0]); hPrintf("%s</A> - %s <BR>\n", row[0], row2[0]); } sqlFreeResult(&sr2); } else { hPrintf("<A HREF=\"http://www.ebi.ac.uk/interpro/entry/%s\" TARGET=_blank>", row[0]); hPrintf("%s</A> - %s<BR>\n", row[0], row[1]); } } hPrintf("<BR>\n"); slFreeList(&list); } if (kgVersion == KG_III) { /* Do Pfam domains here. */ list = getPfamDomainList(conn, geneId); if (list != NULL) { hPrintf("<B>Pfam Domains:</B><BR>"); for (el = list; el != NULL; el = el->next) { char query[256]; char *description; sqlSafef(query, sizeof(query), "select description from pfamDesc where pfamAC='%s'", el->name); description = sqlQuickString(conn, query); if (description == NULL) description = cloneString("n/a"); hPrintf("<A HREF=\"http://pfam.xfam.org/family?acc=%s\" TARGET=_blank>", el->name); hPrintf("%s</A> - %s<BR>\n", el->name, description); freez(&description); } slFreeList(&list); hPrintf("<BR>\n"); } /* Do SCOP domains here */ list = getDomainList(conn, geneId, "Scop"); if (list != NULL) { hPrintf("<B>SCOP Domains:</B><BR>"); for (el = list; el != NULL; el = el->next) { char query[256]; char *description; sqlSafef(query, sizeof(query), "select description from scopDesc where acc='%s'", el->name); description = sqlQuickString(conn, query); if (description == NULL) description = cloneString("n/a"); hPrintf("<A HREF=\"http://scop.berkeley.edu/sunid=%s\" TARGET=_blank>", el->name); hPrintf("%s</A> - %s<BR>\n", el->name, description); freez(&description); } slFreeList(&list); hPrintf("<BR>\n"); } } else { list = spExtDbAcc1List(spConn, swissProtAcc, "Pfam"); if (list != NULL) { char *pfamDescSql = genomeSetting("pfamDescSql"); hPrintf("<B>Pfam Domains:</B><BR>"); for (el = list; el != NULL; el = el->next) { char query[256]; char *description; sqlSafef(query, sizeof(query), pfamDescSql, el->name); description = sqlQuickString(conn, query); if (description == NULL) description = cloneString("n/a"); hPrintf("<A HREF=\"http://pfam.xfam.org/family?acc=%s\" TARGET=_blank>", el->name); hPrintf("%s</A> - %s<BR>\n", el->name, description); freez(&description); } slFreeList(&list); hPrintf("<BR>\n"); } } list = spExtDbAcc1List(spConn, swissProtAcc, "PDB"); if (list != NULL) { struct sqlConnection *conn2 = sqlConnect(db); char query[256], **row; struct sqlResult *sr; int column = 0, maxColumn=3, rowCount=0; hPrintf("<B>Protein Data Bank (PDB) 3-D Structure</B><BR>"); sqlSafef(query, sizeof(query), "select extAcc1,extAcc2 from extDbRef,extDb" " where extDbRef.acc = '%s'" " and extDb.val = 'PDB' and extDb.id = extDbRef.extDb" , swissProtAcc); sr = sqlGetResult(spConn, query); hPrintf("<TABLE><TR>\n"); while ((row = sqlNextRow(sr)) != NULL) { if (++column > maxColumn) { hPrintf("</TR><TR>"); column = 1; if (rowCount == 0) { hPrintf("<TD ALIGN=CENTER COLSPAN=4><I>To conserve bandwidth, only the images from the first %d structures are shown.</I>", maxColumn); hPrintf("</TR><TR>"); } ++rowCount; } hPrintf("<TD>"); hPrintf("<A HREF=\"http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=%s\" TARGET=_blank>", row[0]); if (rowCount < 1) hPrintf("<IMG SRC=\"http://www.rcsb.org/pdb/images/%s_asym_r_250.jpg\"><BR>", row[0]); hPrintf("%s</A> - %s ", row[0], row[1]); // include links LS-SNP and to launch viewer in PDB chimera struct tempName chimerax; lsSnpPdbChimeraSnpAnn(conn, row[0], NULL, &chimerax); hPrintf(" <A HREF=\"%s\">Chimera</A>", chimerax.forHtml); if (lsSnpPdbHasPdb(conn2, row[0])) hPrintf(" <A HREF=\"%s\" TARGET=_blank>LS-SNP</A>", lsSnpPdbGetUrlPdbSnp(row[0], NULL)); hPrintf("</TD>\n"); } hPrintf("</TR></TABLE>\n"); hPrintf("<A href=\"../goldenPath/help/chimera.html\" TARGET=_blank>Chimera help</A>\n"); hPrintf("<BR><BR>\n"); slFreeList(&list); sqlDisconnect(&conn2); } /* Do modBase link. */ { hPrintf("<B>ModBase Predicted Comparative 3D Structure on "); modBaseAnchor(swissProtAcc); hPrintf("%s", swissProtAcc); hPrintf("</A></B><BR>\n"); hPrintf("<TABLE><TR>"); hPrintf("<TD>"); modBaseAnchor(swissProtAcc); hPrintf("\n<IMG SRC=\"https://modbase.compbio.ucsf.edu/modbase-cgi/image/modbase.jpg?database_id=%s\"></A></TD>", swissProtAcc); hPrintf("<TD>"); modBaseAnchor(swissProtAcc); hPrintf("\n<IMG SRC=\"https://modbase.compbio.ucsf.edu/modbase-cgi/image/modbase.jpg?database_id=%s&axis=x°ree=90\"></A></TD>", swissProtAcc); hPrintf("<TD>"); modBaseAnchor(swissProtAcc); hPrintf("\n<IMG SRC=\"https://modbase.compbio.ucsf.edu/modbase-cgi/image/modbase.jpg?database_id=%s&axis=y°ree=90\"></A></TD>", swissProtAcc); hPrintf("</TR><TR>\n"); hPrintf("<TD ALIGN=CENTER>Front</TD>"); hPrintf("<TD ALIGN=CENTER>Top</TD>"); hPrintf("<TD ALIGN=CENTER>Side</TD>"); hPrintf("</TR></TABLE>\n"); hPrintf("<I>The pictures above may be empty if there is no " "ModBase structure for the protein. The ModBase structure " "frequently covers just a fragment of the protein. You may " "be asked to log onto ModBase the first time you click on the " "pictures. It is simplest after logging in to just click on " "the picture again to get to the specific info on that model.</I>"); } }
static void hPrintSpaces(int count) /* Print count number of spaces. */ { while (--count >= 0) hPrintf(" "); }
void startGreatForm() /* Start form for GREAT */ { hPrintf("<FORM ACTION=\"%s\" NAME='greatForm' METHOD=POST>\n", getScriptName()); }
void doGenePredNongenomic(struct sqlConnection *conn, int typeIx) /* Get mrna or protein associated with selected genes. */ { /* Note this does do the whole genome at once rather than one * chromosome at a time, but that's ok because the gene prediction * tracks this serves are on the small side. */ char *typeWords[3]; char *table; struct lm *lm = lmInit(64*1024); int fieldCount; struct bed *bed, *bedList = cookedBedsOnRegions(conn, curTable, getRegions(), lm, &fieldCount); int typeWordCount; textOpen(); /* Figure out which table to use. */ if (isRefGeneTrack(curTable)) { if (typeIx == 1) /* Protein */ doRefGeneProteinSequence(conn, bedList); else doRefGeneMrnaSequence(conn, bedList); } else { char *dupType = cloneString(findTypeForTable(database, curTrack, curTable, ctLookupName)); typeWordCount = chopLine(dupType, typeWords); if (typeIx >= typeWordCount) internalErr(); table = typeWords[typeIx]; if (sqlTableExists(conn, table)) { struct sqlResult *sr; char **row; char query[256]; struct hash *hash = newHash(18); boolean gotResults = FALSE; /* Make hash of all id's passing filters. */ for (bed = bedList; bed != NULL; bed = bed->next) hashAdd(hash, bed->name, NULL); /* Scan through table, outputting ones that match. */ sqlSafef(query, sizeof(query), "select name, seq from %s", table); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { if (hashLookup(hash, row[0])) { hPrintf(">%s\n", row[0]); writeSeqWithBreaks(stdout, row[1], strlen(row[1]), 60); gotResults = TRUE; } } sqlFreeResult(&sr); hashFree(&hash); if (!gotResults) hPrintf(NO_RESULTS); } else { internalErr(); } freez(&dupType); } lmCleanup(&lm); }