Variant Sources:
\n"); for (snpMapSource=0; snpMapSource
\n", snpMapSourceLabels[snpMapSource]); } printf("
Variant Types:
\n"); for (snpMapType=0; snpMapType
\n", snpMapTypeLabels[snpMapType]); } } void snp125OfferGeneTracksForFunction(struct trackDb *tdb) /* Get a list of genePred tracks and make checkboxes to enable hgc's functional * annotations. */ { struct sqlConnection *conn = hAllocConn(database); struct slName *genePredTables = hTrackTablesOfType(conn, "genePred%%"), *gt; if (genePredTables != NULL) { struct trackDb *geneTdbList = NULL, *gTdb; for (gt = genePredTables; gt != NULL; gt = gt->next) { gTdb = hashFindVal(trackHash, gt->name); if (gTdb && sameString(gTdb->grp, "genes")) { // We are going to overwrite gTdb's next pointer and possibly its priority, // so make a shallow copy: gTdb = CloneVar(gTdb); if (gTdb->parent) gTdb->priority = (gTdb->parent->priority + gTdb->priority/1000); slAddHead(&geneTdbList, gTdb); } } slSort(&geneTdbList, trackDbCmp); jsBeginCollapsibleSection(cart, tdb->track, "geneTracks", "Use Gene Tracks for Functional Annotation", FALSE); printf("
On details page, show function and coding differences relative to: \n"); char cartVar[256]; safef(cartVar, sizeof(cartVar), "%s_geneTrack", tdb->track); jsMakeCheckboxGroupSetClearButton(cartVar, TRUE); jsMakeCheckboxGroupSetClearButton(cartVar, FALSE); struct slName *selectedGeneTracks = cartOptionalSlNameList(cart, cartVar); if (!cartListVarExists(cart, cartVar)) { char *defaultGeneTracks = trackDbSetting(tdb, "defaultGeneTracks"); if (isNotEmpty(defaultGeneTracks)) selectedGeneTracks = slNameListFromComma(defaultGeneTracks); } int numCols = 4, i; int menuSize = slCount(geneTdbList); char **values = needMem(menuSize*sizeof(char *)); char **labels = needMem(menuSize*sizeof(char *)); for (i = 0, gTdb = geneTdbList; i < menuSize && gTdb != NULL; i++, gTdb = gTdb->next) { values[i] = gTdb->track; labels[i] = gTdb->shortLabel; } cgiMakeCheckboxGroupWithVals(cartVar, labels, values, menuSize, selectedGeneTracks, numCols); jsEndCollapsibleSection(); } hFreeConn(&conn); } #define SNP125_FILTER_COLUMNS 4 #define SNP125_DEFAULTS "snp125Defaults" void snp125PrintFilterControls(char *track, char *attributeLabel, char *attributeVar, char *labels[], char *values[], int menuSize) /* Print two or more rows (attribute name header and row(s) of checkboxes) * of a table displaying snp125 attribute filter checkboxes. */ { char anchor[256]; safecpy(anchor, sizeof(anchor), attributeVar); anchor[0] = toupper(anchor[0]); printf("
\n"); safef(cartVar, sizeof(cartVar), "%s.minAvHet", tdb->track); double minAvHet = cartUsualDouble(cart, cartVar, // Check old cart var name: cartUsualDouble(cart, "snp125AvHetCutoff", SNP125_DEFAULT_MIN_AVHET)); printf("Minimum Average Heterozygosity: "); cgiMakeDoubleVar(cartVar, minAvHet, 6); printf("
\n"); safef(cartVar, sizeof(cartVar), "%s.maxWeight", tdb->track); int defaultMaxWeight = SNP125_DEFAULT_MAX_WEIGHT; char *setting = trackDbSetting(tdb, "defaultMaxWeight"); if (isNotEmpty(setting)) defaultMaxWeight = atoi(setting); int maxWeight = cartUsualInt(cart, cartVar, // Check old cart var name: cartUsualInt(cart, "snp125WeightCutoff", defaultMaxWeight)); printf("Maximum Weight: "); cgiMakeIntVar(cartVar, maxWeight, 4); printf(" Range: 1, 2 or 3; SNPs with higher weights are less reliable
\n"); if (version >= 132) { printf("Minimum number of distinct " "Submitters: "); safef(cartVar, sizeof(cartVar), "%s.minSubmitters", tdb->track); cgiMakeIntVar(cartVar, cartUsualInt(cart, cartVar, SNP132_DEFAULT_MIN_SUBMITTERS), 4); printf("
\n"); printf("Minor Allele Frequency range: "); safef(cartVar, sizeof(cartVar), "%s.minMinorAlFreq", tdb->track); float maf = cartUsualDouble(cart, cartVar, SNP132_DEFAULT_MIN_MINOR_AL_FREQ); cgiMakeDoubleVarInRange(cartVar, maf, NULL, 4, "0.0", "0.5"); printf(" to "); safef(cartVar, sizeof(cartVar), "%s.maxMinorAlFreq", tdb->track); maf = cartUsualDouble(cart, cartVar, SNP132_DEFAULT_MAX_MINOR_AL_FREQ); cgiMakeDoubleVarInRange(cartVar, maf, NULL, 4, "0.0", "0.5"); printf(" Range: 0.0 - 0.5\n"); printf("
\n"); printf("Minimum chromosome sample count (2N) for " "Allele Frequency data: "); safef(cartVar, sizeof(cartVar), "%s.minAlFreq2N", tdb->track); cgiMakeIntVar(cartVar, cartUsualInt(cart, cartVar, SNP132_DEFAULT_MIN_AL_FREQ_2N), 4); printf("
\n"); } printf("
\n"); printf("Filter by attribute:
\n"); printf("Check the boxes below to include SNPs with those attributes. " "In order to be displayed, a SNP must pass the filter for each " "category. \n" "Some assemblies may not contain any SNPs that have some of the " "listed attributes.\n" "
\n"); printf("
\n"); printf("
| %s | ", labels[i]); char cartVar[512]; safef(cartVar, sizeof(cartVar), "%s.%s%s", track, attribute, (varsAreOld ? snp125OldColorVarToNew(vars[i], attribute) : vars[i])); char *defaultCol = defaults[i]; if (varsAreOld) defaultCol = cartUsualString(cart, vars[i], defaultCol); char *selected = cartUsualString(cart, cartVar, defaultCol); cgiMakeDropListWithVals(cartVar, snp125ColorLabel, snp125ColorLabel, snp125ColorArraySize, selected); printf(" | "); } printf(" |
SNP Feature for Color Specification:\n"); char **labels = snp132ColorSourceLabels; int arraySize = snp132ColorSourceArraySize; if (version <= 127) { labels = snp125ColorSourceLabels; arraySize = snp125ColorSourceArraySize; } else if (version <= 131) { labels = snp128ColorSourceLabels; arraySize = snp128ColorSourceArraySize; } // It would be preferable for Javascript to handle changing the color selection // menus when the color source selection changes, but for now we do a submit that // returns to the current vertical position: char autoSubmit[2048]; safef(autoSubmit, sizeof(autoSubmit), "onchange=\"" "document."MAIN_FORM".action = '%s'; %s" "document."MAIN_FORM".submit();\"", cgiScriptName(), jsSetVerticalPosition(MAIN_FORM)); cgiContinueHiddenVar("g"); cgiContinueHiddenVar("c"); char cartVar[512]; safef(cartVar, sizeof(cartVar), "%s.colorSource", tdb->track); enum snp125ColorSource colorSourceCart = snp125ColorSourceFromCart(cart, tdb); char *colorSourceSelected = snp125ColorSourceToLabel(tdb, colorSourceCart); cgiMakeDropListFull(cartVar, labels, labels, arraySize, colorSourceSelected, autoSubmit); printf(" \n"); char javascript[2048]; safef(javascript, sizeof(javascript), "document."MAIN_FORM".action='%s'; %s document."MAIN_FORM".submit();", cgiScriptName(), jsSetVerticalPosition(MAIN_FORM)); cgiMakeOnClickSubmitButton(javascript, defaultButtonVar, JS_DEFAULTS_BUTTON_LABEL); printf("
\n" "The selected "Feature for Color Specification" above has the\n" "selection of colors below for each attribute. Only the color\n" "options for the feature selected above will be used to color items;\n" "color options for other features will not be shown.\n"); if (version > 127 && colorSourceCart == snp125ColorSourceLocType) colorSourceCart = SNP125_DEFAULT_COLOR_SOURCE; switch (colorSourceCart) { int funcArraySize; case snp125ColorSourceLocType: snp125PrintColorSpec(tdb->track, "locType", snp125LocTypeOldColorVars, TRUE, snp125LocTypeLabels, snp125LocTypeDefault, snp125LocTypeArraySize); break; case snp125ColorSourceClass: snp125PrintColorSpec(tdb->track, "class", snp125ClassOldColorVars, TRUE, snp125ClassLabels, snp125ClassDefault, snp125ClassArraySize); break; case snp125ColorSourceValid: snp125PrintColorSpec(tdb->track, "valid", snp125ValidOldColorVars, TRUE, snp125ValidLabels, snp125ValidDefault, snp125ValidArraySize); break; case snp125ColorSourceFunc: funcArraySize = (version < 130) ? snp125FuncArraySize : (snp125FuncArraySize - 1); snp125PrintColorSpec(tdb->track, "func", snp125FuncOldColorVars, TRUE, snp125FuncLabels, snp125FuncDefault, funcArraySize); break; case snp125ColorSourceMolType: snp125PrintColorSpec(tdb->track, "molType", snp125MolTypeOldColorVars, TRUE, snp125MolTypeLabels, snp125MolTypeDefault, snp125MolTypeArraySize); break; case snp125ColorSourceExceptions: snp125PrintColorSpec(tdb->track, "exceptions", snp132ExceptionVarName, FALSE, snp132ExceptionLabels, snp132ExceptionDefault, snp132ExceptionArraySize); break; case snp125ColorSourceBitfields: snp125PrintColorSpec(tdb->track, "bitfields", snp132BitfieldVarName, FALSE, snp132BitfieldLabels, snp132BitfieldDefault, snp132BitfieldArraySize); break; case snp125ColorSourceAlleleFreq: printf("
Items are be colored by allele frequency on a red-blue spectrum, " "with red representing rare alleles and blue representing common alleles. " "Items with no allele frequency data are colored black.
"); break; default: errAbort("Unrecognized value of enum snp125ColorSource (%d)", colorSourceCart); } jsEndCollapsibleSection(); } void snp125Ui(struct trackDb *tdb) /* UI for dbSNP version 125 and later. */ { char *orthoTable = snp125OrthoTable(tdb, NULL); int version = snpVersion(tdb->track); char cartVar[512]; jsInit(); if (version < 130) snp125ValidArraySize--; // no by-1000genomes if (isNotEmpty(orthoTable) && hTableExists(database, orthoTable)) { printf("Include Chimp state and observed human alleles in name: "); safef(cartVar, sizeof(cartVar), "%s.extendedNames", tdb->track); snp125ExtendedNames = cartUsualBoolean(cart, cartVar, // Check old cart var name for backwards compatibility w/ old sessions: cartUsualBoolean(cart, "snp125ExtendedNames", FALSE)); cgiMakeCheckBox(cartVar, snp125ExtendedNames); printf("
(If enabled, chimp allele is displayed first, then '>', then human alleles)."); printf("
\n"); } else puts("
"); // Make wrapper table for collapsible sections: puts("
Colors and Filters:\n"); printf("
Use the "Color Specification" buttons to specify a group to direct coloring for the track display.\n"); printf("
Variants can optionally be excluded based on their values in each of the subsequent categories by choosing "exclude".\n"); printf("
\n"); printf("
Color Specification:
\n"); snpColorSourceCart[0] = cartUsualString(cart, snpColorSourceDataName[0], snpColorSourceDefault[0]); snpColorFilterButtons(snpColorSourceDataName[0], snpColorSourceCart[0]); snpAvHetCutoff = atof(cartUsualString(cart, "snpAvHetCutoff", "0")); printf("
Minimum Average Heterozygosity: "); cgiMakeDoubleVar("snpAvHetCutoff",snpAvHetCutoff,6); printf("
Exclude | Sources:
\n"); for (snpSource=0; snpSource < snpSourceCartSize; snpSource++) { snpSourceCart[snpSource] = cartUsualString(cart, snpSourceStrings[snpSource], snpSourceDefault[snpSource]); snpFilterButtons(snpSourceStrings[snpSource], snpSourceCart[snpSource]); printf(" - %s
\n", snpSourceLabels[snpSource]); } printf("
Exclude | Molecule Types:
\n"); for (snpMolType=0; snpMolType
\n", snpMolTypeLabels[snpMolType]); } printf("
Exclude | Variant Classes:
\n"); for (snpClass=0; snpClass
\n", snpClassLabels[snpClass]); } printf("
Exclude | Validation Status:
\n"); for (snpValid=0; snpValid
\n",snpValidLabels[snpValid]); } printf("
Exclude | Functional Classes:
\n"); for (snpFunc=0; snpFunc
\n",snpFuncLabels[snpFunc]); } printf("
Exclude | Location Type:
\n"); for (snpLocType=0; snpLocType
\n",snpLocTypeLabels[snpLocType]); } } void ldUi(struct trackDb *tdb) /* Put up UI snp data. */ { char var[512]; char *val; /* It would be nice to add a 'reset' button to reset the ld variables to their defaults. */ printf("
LD Values:
\n"); safef(var, sizeof(var), "%s_val", tdb->track); val = cartUsualString(cart, var, ldValDefault); cgiMakeRadioButton(var, "rsquared", sameString("rsquared", val)); printf(" r2 "); cgiMakeRadioButton(var, "dprime", sameString("dprime", val)); printf(" D' "); cgiMakeRadioButton(var, "lod", sameString("lod", val)); printf(" LOD
"); printf("
Track Geometry:
\n"); safef(var, sizeof(var), "%s_trm", tdb->track); cgiMakeCheckBox(var, cartUsualBoolean(cart, var, ldTrmDefault)); printf(" Trim to triangle
\n"); if (tdbIsComposite(tdb)) { printf("
"); struct slRef *tdbRefList = trackDbListGetRefsToDescendantLeaves(tdb->subtracks); slSort(&tdbRefList, trackDbRefCmp); struct slRef *tdbRef; for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next) { struct trackDb *subTdb = tdbRef->val; if (hTableExists(database, subTdb->table)) { safef(var, sizeof(var), "%s_inv", subTdb->track); cgiMakeCheckBoxJS(var, cartUsualBoolean(cart, var, ldInvDefault), "class='subtrackInCompositeUi'"); printf(" Invert display for %s
\n", subTdb->longLabel); } } slFreeList(&tdbRefList); } else { safef(var, sizeof(var), "%s_inv", tdb->track); printf(" "); cgiMakeCheckBox(var, cartUsualBoolean(cart, var, ldInvDefault)); printf(" Invert the display
\n"); } printf("
Colors:\n"); safef(var, sizeof(var), "%s_pos", tdb->track); val = cartUsualString(cart, var, ldPosDefault); printf("
| LD values | \n- "); radioButton(var, val, "red"); printf(" | \n"); radioButton(var, val, "green"); printf(" | \n"); radioButton(var, val, "blue"); printf(" | \n||||
| Outlines | \n- "); radioButton(var, val, "red"); printf(" | \n"); radioButton(var, val, "green"); printf(" | \n"); radioButton(var, val, "blue"); printf(" | \n"); radioButton(var, val, "yellow"); printf(" | \n"); radioButton(var, val, "black"); printf(" | \n"); radioButton(var, val, "white"); printf(" | \n"); radioButton(var, val, "none"); printf(" | \n
\n"); } if (tdbIsComposite(tdb)) printf("
Populations:\n"); } void oregannoUi (struct trackDb *tdb) /* print the controls */ { int i = 0; /* variable to walk through array */ printf("
Type of region to display: "); printf(" (Click here for detailed information on these element types)
"); for (i = 0; i < oregannoTypeSize; i++) { cartMakeCheckBox(cart, oregannoTypeString[i], TRUE); printf (" %s
", oregannoTypeLabel[i]); } } void labelMakeCheckBox(struct trackDb *tdb, char *sym, char *desc, boolean dflt) /* add a checkbox use to choose labels to enable. */ { char varName[64]; safef(varName, sizeof(varName), "%s.label.%s", tdb->track, sym); boolean option = cartUsualBoolean(cart, varName, dflt); cgiMakeCheckBox(varName, option); printf(" %s ", desc); } void gvIdControls (struct trackDb *tdb) /* print the controls for the label choice */ { printf("Label: "); labelMakeCheckBox(tdb, "hgvs", "HGVS name", FALSE); labelMakeCheckBox(tdb, "common", "Common name", FALSE); printf("
\n"); } void gvUi(struct trackDb *tdb) /* print UI for human mutation filters */ { int i = 0; /* variable to walk through arrays */ //char *def; gvIdControls(tdb); /* printf("
Exclude data source
"); for (i = 0; i < gvSrcSize; i++) { if (differentString(gvSrcDbValue[i], "LSDB")) { if (sameString(gvSrcDbValue[i], "UniProt (Swiss-Prot/TrEMBL)")) { // exclude Swiss-Prot data by default, can be misleading cartMakeCheckBox(cart, gvSrcString[i], TRUE); } else { cartMakeCheckBox(cart, gvSrcString[i], FALSE); } printf (" %s
", gvSrcDbValue[i]); // label with db value } else { cartMakeCheckBox(cart, gvSrcString[i], FALSE); printf (" Locus Specific Databases
"); } } */ printf("
Exclude
"); for (i = 0; i < gvAccuracySize; i++) { cartMakeCheckBox(cart, gvAccuracyString[i], FALSE); printf (" %s
", gvAccuracyLabel[i]); } printf("
Exclude mutation type
"); for (i = 0; i < gvTypeSize; i++) { cartMakeCheckBox(cart, gvTypeString[i], FALSE); printf (" %s
", gvTypeLabel[i]); } printf("
Exclude mutation location
"); for (i = 0; i < gvLocationSize; i++) { cartMakeCheckBox(cart, gvLocationString[i], FALSE); printf (" %s
", gvLocationLabel[i]); } /* printf("
Exclude phenotype association
"); for (i = 0; i < gvFilterDASize; i++) { cartMakeCheckBox(cart, gvFilterDAString[i], FALSE); printf (" %s
", gvFilterDALabel[i]); } */ printf("
"); cartMakeRadioButton(cart, "gvPos.filter.colorby", "type", "type"); printf("Color mutations by type
"); for (i = 0; i < gvColorTypeSize; i++) { char *defaultVal = cartUsualString(cart, gvColorTypeStrings[i], gvColorTypeDefault[i]); printf (" %s ", gvColorTypeLabels[i]); cgiMakeDropList(gvColorTypeStrings[i], gvColorLabels, gvColorLabelSize, defaultVal); } printf("
"); /* cartMakeRadioButton(cart, "gvPos.filter.colorby", "disease", "type"); printf("Color mutations by phenotype association (determination is described below)
"); for (i = 0; i < gvColorDASize; i++) { char *defaultVal = cartUsualString(cart, gvColorDAStrings[i], gvColorDADefault[i]); printf (" %s ", gvColorDALabels[i]); cgiMakeDropList(gvColorDAStrings[i], gvColorLabels, gvColorLabelSize, defaultVal); } printf("
"); */ /* only on development page for now, but need to check in other changes */ /* if (startsWith("hgwdev-giardine", cgiServerName())) { cartMakeRadioButton(cart, "gvPos.filter.colorby", "count", "type"); printf("Color mutations by count of positions associated with a mutation
"); def = cartUsualString(cart, "gvColorCountSingle", "blue"); printf (" Single position "); cgiMakeDropList("gvColorCountSingle", gvColorLabels, gvColorLabelSize, def); def = cartUsualString(cart, "gvColorCountMult", "green"); printf (" Multiple positions "); cgiMakeDropList("gvColorCountMult", gvColorLabels, gvColorLabelSize, def); printf("
"); } */ } void retroposonsUi(struct trackDb *tdb) { struct sqlConnection *conn = hAllocConn(database); char query[256]; char **row; struct sqlResult *sr; struct slName *sList = NULL, *item; int menuSize = 0; char **menu; int i; char *tableList[3]; i = 0; tableList[i++] = "dbRIPAlu"; tableList[i++] = "dbRIPL1"; tableList[i++] = "dbRIPSVA"; safef(query, sizeof(query), "SELECT genoRegion FROM dbRIPAlu GROUP BY genoRegion ORDER BY genoRegion DESC"); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { slNameAddHead(&sList, row[0]); } sqlFreeResult(&sr); menuSize = slCount(sList) + 1; menu = needMem((size_t)(menuSize * sizeof(char *))); i = 0; menu[i++] = GENO_REGION_DEFAULT; for (item = sList; item != NULL; item = item->next) menu[i++] = item->name; puts("
Add filters:
\n" );
puts("Gene Context: " );
cgiMakeDropList(GENO_REGION, menu, menuSize,
cartCgiUsualString(cart, GENO_REGION, menu[0]));
slFreeList(&sList);
freez(&menu);
menuSize = 3;
menu = needMem((size_t)(menuSize * sizeof(char *)));
i = 0;
menu[i++] = POLY_SOURCE_DEFAULT;
menu[i++] = "yes";
menu[i++] = "no";
puts("
\nInsertion found in reference sequence: ");
cgiMakeDropList(POLY_SOURCE, menu, menuSize,
cartCgiUsualString(cart, POLY_SOURCE, menu[0]));
freez(&menu);
for (i = 0; i < 3; ++i)
{
safef(query, sizeof(query),
"SELECT polySubfamily FROM %s GROUP BY polySubfamily ORDER BY polySubfamily DESC", tableList[i]);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
slNameStore(&sList, row[0]);
}
sqlFreeResult(&sr);
}
slNameSortCase(&sList);
menuSize = slCount(sList) + 1;
menu = needMem((size_t)(menuSize * sizeof(char *)));
i = 0;
menu[i++] = POLY_SUBFAMILY_DEFAULT;
for (item = sList; item != NULL; item = item->next)
menu[i++] = item->name;
puts("
\nInsertion identified in sub-family: ");
cgiMakeDropList(POLY_SUBFAMILY, menu, menuSize,
cartCgiUsualString(cart, POLY_SUBFAMILY, menu[0]));
slFreeList(&sList);
freez(&menu);
safef(query, sizeof(query),
"SELECT ethnicGroup FROM polyGenotype GROUP BY ethnicGroup ORDER BY ethnicGroup DESC");
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
slNameStore(&sList, row[0]);
}
sqlFreeResult(&sr);
menuSize = slCount(sList) + 1;
menu = needMem((size_t)(menuSize * sizeof(char *)));
i = 0;
menu[i++] = ETHNIC_GROUP_DEFAULT;
for (item = sList; item != NULL; item = item->next)
menu[i++] = item->name;
puts("
\nEthnic group: ");
cgiMakeDropList(ETHNIC_GROUP, menu, menuSize,
cartCgiUsualString(cart, ETHNIC_GROUP, menu[0]));
slFreeList(&sList);
freez(&menu);
puts(" ");
radioButton(ETHNIC_GROUP_EXCINC,
cartUsualString(cart, ETHNIC_GROUP_EXCINC, ETHNIC_NOT_DEFAULT),
"include");
radioButton(ETHNIC_GROUP_EXCINC,
cartUsualString(cart, ETHNIC_GROUP_EXCINC, ETHNIC_NOT_DEFAULT),
"exclude");
puts("this ethnic group
\n");
#ifdef HAS_NO_MEANING
menuSize = 10;
menu = needMem((size_t)(menuSize * sizeof(char *)));
i = 0;
menu[i++] = "0.0"; menu[i++] = "0.1"; menu[i++] = "0.2"; menu[i++] = "0.3";
menu[i++] = "0.4"; menu[i++] = "0.5"; menu[i++] = "0.6"; menu[i++] = "0.7";
menu[i++] = "0.8"; menu[i++] = "0.9";
/* safety check on bad user input, they may have set them illegally
* in which case reset them to defaults 0.0 <= f <= 1.0
*/
double freqLow = sqlFloat(cartCgiUsualString(cart, ALLELE_FREQ_LOW, menu[0]));
double freqHi = sqlFloat(cartCgiUsualString(cart, ALLELE_FREQ_HI, menu[9]));
puts("
\nRestrict polymorphism frequency to: ");
if (freqLow < freqHi)
cgiMakeDropList(ALLELE_FREQ_LOW, menu, menuSize,
cartCgiUsualString(cart, ALLELE_FREQ_LOW, menu[0]));
else
cgiMakeDropList(ALLELE_FREQ_LOW, menu, menuSize, menu[0]);
i = 0;
menu[i++] = "0.1"; menu[i++] = "0.2"; menu[i++] = "0.3"; menu[i++] = "0.4";
menu[i++] = "0.5"; menu[i++] = "0.6"; menu[i++] = "0.7"; menu[i++] = "0.8";
menu[i++] = "0.9"; menu[i++] = "1.0";
puts(" <= f <= ");
if (freqLow < freqHi)
cgiMakeDropList(ALLELE_FREQ_HI, menu, menuSize,
cartCgiUsualString(cart, ALLELE_FREQ_HI, menu[9]));
else
cgiMakeDropList(ALLELE_FREQ_HI, menu, menuSize, menu[9]);
freez(&menu);
#endif /* HAS_NO_MEANING */
menuSize = 3;
menu = needMem((size_t)(menuSize * sizeof(char *)));
i = 0;
menu[i++] = DISEASE_DEFAULT;
menu[i++] = "yes";
menu[i++] = "no";
puts("
\nAssociated disease state known: ");
cgiMakeDropList(dbRIP_DISEASE, menu, menuSize,
cartCgiUsualString(cart, dbRIP_DISEASE, menu[0]));
freez(&menu);
puts("\n
Temporary Intronerator link: %s:%d-%d for testing purposes only \n
", chromosome+3, start, end, chromosome+3, start, end ); */ } void fishClonesUi(struct trackDb *tdb) /* Put up UI fishClones. */ { char *fishClonesFilter = cartUsualString(cart, "fishClones.filter", "red"); char *fishClonesMap = cartUsualString(cart, "fishClones.type", fcoeEnumToString(0)); filterButtons("fishClones.filter", fishClonesFilter, TRUE); printf(" "); fcoeDropDown("fishClones.type", fishClonesMap); } void recombRateUi(struct trackDb *tdb) /* Put up UI recombRate. */ { char *recombRateMap = cartUsualString(cart, "recombRate.type", rroeEnumToString(0)); printf("Map Distances: "); rroeDropDown("recombRate.type", recombRateMap); } void recombRateRatUi(struct trackDb *tdb) /* Put up UI recombRateRat. */ { char *recombRateRatMap = cartUsualString(cart, "recombRateRat.type", rrroeEnumToString(0)); printf("Map Distances: "); rrroeDropDown("recombRateRat.type", recombRateRatMap); } void recombRateMouseUi(struct trackDb *tdb) /* Put up UI recombRateMouse. */ { char *recombRateMouseMap = cartUsualString(cart, "recombRateMouse.type", rrmoeEnumToString(0)); printf("Map Distances: "); rrmoeDropDown("recombRateMouse.type", recombRateMouseMap); } void cghNci60Ui(struct trackDb *tdb) /* Put up UI cghNci60. */ { char *cghNci60Map = cartUsualString(cart, "cghNci60.type", cghoeEnumToString(0)); char *col = cartUsualString(cart, "cghNci60.color", "gr"); printf(" Cell Lines: "); cghoeDropDown("cghNci60.type", cghNci60Map); printf(" "); printf(" Color Scheme: "); cgiMakeRadioButton("cghNci60.color", "gr", sameString(col, "gr")); printf(" green/red "); cgiMakeRadioButton("cghNci60.color", "rg", sameString(col, "rg")); printf(" red/green "); cgiMakeRadioButton("cghNci60.color", "rb", sameString(col, "rb")); printf(" red/blue "); } void affyUi(struct trackDb *tdb) /* put up UI for the affy track from stanford track */ { char *affyMap; char *col; char varName[128]; safef(varName, sizeof(varName), "%s.%s", tdb->track, "type"); affyMap = cartUsualString(cart, varName, affyEnumToString(affyTissue)); col = cartUsualString(cart, "exprssn.color", "rg"); printf("Experiment Display: ");
affyDropDown(varName, affyMap);
printf(" Color Scheme: ");
cgiMakeRadioButton("exprssn.color", "rg", sameString(col, "rg"));
printf(" red/green ");
cgiMakeRadioButton("exprssn.color", "rb", sameString(col, "rb"));
printf(" red/blue ");
}
void expRatioCombineDropDown(struct trackDb *tdb, struct microarrayGroups *groups)
/* Make a drop-down of all the main combinations. */
{
struct maGrouping *comb;
int size = 0;
int i;
char **menuArray;
char **valArray;
char *dropDownName = expRatioCombineDLName(tdb->track);
char *defaultSelection = NULL;
char *cartSetting = NULL;
if (!groups->allArrays)
errAbort("The \'all\' stanza must be set in the microarrayGroup settings for track %s", tdb->track);
if (groups->defaultCombine)
defaultSelection = groups->defaultCombine->name;
else
defaultSelection = groups->allArrays->name;
size = groups->numCombinations + 1;
AllocArray(menuArray, size);
AllocArray(valArray, size);
menuArray[0] = groups->allArrays->description;
valArray[0] = groups->allArrays->name;
for (i = 1, comb = groups->combineSettings; (i < size) && (comb != NULL); i++, comb = comb->next)
{
menuArray[i] = cloneString(comb->description);
valArray[i] = cloneString(comb->name);
}
cartSetting = cartUsualString(cart, dropDownName, defaultSelection);
printf(" Combine arrays: ");
cgiMakeDropListWithVals(dropDownName, menuArray, valArray,
size, cartSetting);
}
void expRatioDrawExonOption(struct trackDb *tdb)
/* Add option to show exons if possible. */
{
char checkBoxName[512];
char *drawExons = trackDbSetting(tdb, "expDrawExons");
boolean checked = FALSE;
if (!drawExons || differentWord(drawExons, "on"))
return;
safef(checkBoxName, sizeof(checkBoxName), "%s.expDrawExons", tdb->track);
checked = cartCgiUsualBoolean(cart, checkBoxName, FALSE);
puts("Draw intron lines/arrows and exons: ");
cgiMakeCheckBox(checkBoxName, checked);
puts("
\n");
}
void expRatioColorOption(struct trackDb *tdb)
/* Radio button for red/green or blue/yellow */
{
char radioName[256];
char *colorSetting = NULL;
char *tdbSetting = trackDbSettingOrDefault(tdb, "expColor", "redGreen");
safef(radioName, sizeof(radioName), "%s.color", tdb->track);
colorSetting = cartUsualString(cart, radioName, tdbSetting);
puts("
Color:
");
cgiMakeRadioButton(radioName, "redGreen", sameString(colorSetting, "redGreen"));
puts("red/green
");
cgiMakeRadioButton(radioName, "redBlue", sameString(colorSetting, "redBlue"));
puts("red/blue
");
cgiMakeRadioButton(radioName, "yellowBlue", sameString(colorSetting, "yellowBlue"));
puts("yellow/blue
\n");
cgiMakeRadioButton(radioName, "redBlueOnWhite", sameString(colorSetting, "redBlueOnWhite"));
puts("red/blue on white background
");
cgiMakeRadioButton(radioName, "redBlueOnYellow", sameString(colorSetting, "redBlueOnYellow"));
puts("red/blue on yellow background
");
}
void expRatioSubsetDropDown(struct maGrouping *ss, char *varName, char *offset)
/* because setting up the droplist is a bit involved... this is just called */
/* from expRatioSubsetOptions() */
{
char **menu;
char **values;
int i;
AllocArray(menu, ss->numGroups);
AllocArray(values, ss->numGroups);
for (i = 0; i < ss->numGroups; i++)
{
char num[4];
safef(num, sizeof(num), "%d", i);
menu[i] = cloneString(ss->names[i]);
values[i] = cloneString(num);
}
cgiMakeDropListWithVals(varName, menu, values, ss->numGroups, offset);
}
void expRatioSubsetOptions(struct trackDb *tdb, struct microarrayGroups *groups)
/* subsetting options for a microarray track */
{
char *radioVarName = expRatioSubsetRadioName(tdb->track, groups);
char *subSetting = NULL;
struct maGrouping *subsets = groups->subsetSettings;
struct maGrouping *ss;
subSetting = cartUsualString(cart, radioVarName, NULL);
puts("
Subset:
");
cgiMakeRadioButton(radioVarName, "none", (subSetting == NULL) || sameString(subSetting, "none"));
puts("no subset
\n");
for (ss = subsets; ss != NULL; ss = ss->next)
{
char *dropVarName = expRatioSubsetDLName(tdb->track, ss);
char *offS = NULL;
offS = cartUsualString(cart, dropVarName, "-1");
cgiMakeRadioButton(radioVarName, ss->name, (subSetting) && sameString(ss->name, subSetting));
printf("%s \n", ss->description);
expRatioSubsetDropDown(ss, dropVarName, offS);
printf("
\n");
}
}
void expRatioUi(struct trackDb *tdb)
/* UI options for the expRatio tracks. */
{
struct microarrayGroups *groups = maGetTrackGroupings(database, tdb);
if (groups == NULL)
errAbort("Could not get group settings for track.");
expRatioDrawExonOption(tdb);
if (groups->numCombinations > 0)
expRatioCombineDropDown(tdb, groups);
if (groups->numSubsets > 0)
expRatioSubsetOptions(tdb, groups);
expRatioColorOption(tdb);
}
void expRatioCtUi(struct trackDb *tdb)
/* UI options for array custom tracks. */
{
expRatioColorOption(tdb);
}
void affyAllExonUi(struct trackDb *tdb)
/* put up UI for the affy all exon tracks. */
{
char *affyAllExonMap;
char *col;
char varName[128];
safef(varName, sizeof(varName), "%s.%s", tdb->track, "type");
affyAllExonMap = cartUsualString(cart, varName, affyAllExonEnumToString(affyAllExonTissue));
col = cartUsualString(cart, "exprssn.color", "rg");
printf("
Experiment Display: "); affyAllExonDropDown(varName, affyAllExonMap); printf(" Color Scheme: "); cgiMakeRadioButton("exprssn.color", "rg", sameString(col, "rg")); printf(" red/green "); cgiMakeRadioButton("exprssn.color", "rb", sameString(col, "rb")); printf(" red/blue "); } void rosettaUi(struct trackDb *tdb) /* put up UI for the rosetta track */ { char *rosettaMap = cartUsualString(cart, "rosetta.type", rosettaEnumToString(0)); char *col = cartUsualString(cart, "exprssn.color", "rg"); char *exonTypes = cartUsualString(cart, "rosetta.et", rosettaExonEnumToString(0)); printf("
Reference Sample: "); rosettaDropDown("rosetta.type", rosettaMap); printf(" "); printf("Exons Shown: "); rosettaExonDropDown("rosetta.et", exonTypes); printf(" Color Scheme: "); cgiMakeRadioButton("exprssn.color", "rg", sameString(col, "rg")); printf(" red/green "); cgiMakeRadioButton("exprssn.color", "rb", sameString(col, "rb")); printf(" red/blue "); } void switchDbScoreUi(struct trackDb *tdb) /* Put up UI for filtering switchDb track based on a score */ /* The scores use a drop-box to set scoreFilter at several */ /* thresholds. */ { char *option = "switchDbTss.scoreFilter"; char *pseudo = "switchDbTss.pseudo"; char *menu[3] = {"All TSSs (no filter)", "Lower stringency (score >= 10)", "Higher stringency (score >= 20)"}; char *values[3] = {"0", "10", "20"}; char *scoreValString = trackDbSetting(tdb, "scoreFilter"); int scoreSetting; int scoreVal = SWITCHDBTSS_FILTER; char tempScore[256]; if (scoreValString != NULL) scoreVal = atoi(scoreValString); printf("
Filter TSSs by score: "); scoreSetting = cartUsualInt(cart, option, scoreVal); safef(tempScore, sizeof(tempScore), "%d",scoreSetting); cgiMakeDropListWithVals(option, menu, values, ArraySize(menu), tempScore); printf("
Include TSSs for predicted pseudogenes "); cartMakeCheckBox(cart, pseudo, FALSE); } void blastSGUi(struct trackDb *tdb) { char geneName[64]; char accName[64]; char sprotName[64]; char posName[64]; char cModeStr[64]; boolean useGene, useAcc, useSprot, usePos; int cMode; char *cModes[3] = {"0", "1", "2"}; safef(geneName, sizeof(geneName), "%s.geneLabel", tdb->track); safef(accName, sizeof(accName), "%s.accLabel", tdb->track); safef(sprotName, sizeof(sprotName), "%s.sprotLabel", tdb->track); safef(posName, sizeof(posName), "%s.posLabel", tdb->track); useGene= cartUsualBoolean(cart, geneName, TRUE); useAcc= cartUsualBoolean(cart, accName, FALSE); useSprot= cartUsualBoolean(cart, sprotName, FALSE); usePos= cartUsualBoolean(cart, posName, FALSE); safef(cModeStr, sizeof(cModeStr), "%s.cmode", tdb->track); cMode = cartUsualInt(cart, cModeStr, 0); printf("
Color elements: "); cgiMakeRadioButton(cModeStr, cModes[0], cMode == 0); printf("by score "); cgiMakeRadioButton(cModeStr, cModes[1], cMode == 1); printf("by yeast chromosome "); cgiMakeRadioButton(cModeStr, cModes[2], cMode == 2); printf("black"); printf("
Label elements by: "); cgiMakeCheckBox(geneName, useGene); printf("Yeast Gene "); cgiMakeCheckBox(accName, useAcc); printf("Yeast mRNA "); cgiMakeCheckBox(sprotName, useSprot); printf("SwissProt ID "); cgiMakeCheckBox(posName, usePos); printf("Yeast Position"); baseColorDrawOptDropDown(cart, tdb); } void blastFBUi(struct trackDb *tdb) { char geneName[64]; char accName[64]; char sprotName[64]; char posName[64]; char cModeStr[64]; boolean useGene, useAcc, usePos; int cMode; char *cModes[3] = {"0", "1", "2"}; safef(geneName, sizeof(geneName), "%s.geneLabel", tdb->track); safef(accName, sizeof(accName), "%s.accLabel", tdb->track); safef(sprotName, sizeof(sprotName), "%s.sprotLabel", tdb->track); safef(posName, sizeof(posName), "%s.posLabel", tdb->track); useGene= cartUsualBoolean(cart, geneName, TRUE); useAcc= cartUsualBoolean(cart, accName, FALSE); usePos= cartUsualBoolean(cart, posName, FALSE); safef(cModeStr, sizeof(cModeStr), "%s.cmode", tdb->track); cMode = cartUsualInt(cart, cModeStr, 0); printf("
Color elements: "); cgiMakeRadioButton(cModeStr, cModes[0], cMode == 0); printf("by score "); cgiMakeRadioButton(cModeStr, cModes[1], cMode == 1); printf("by D. mel. chromosome "); cgiMakeRadioButton(cModeStr, cModes[2], cMode == 2); printf("black"); printf("
Label elements by: "); cgiMakeCheckBox(geneName, useGene); printf("FlyBase Gene "); cgiMakeCheckBox(accName, useAcc); printf("D. melanogaster mRNA "); cgiMakeCheckBox(posName, usePos); printf("D. melanogaster Position"); baseColorDrawOptDropDown(cart, tdb); } void blastUi(struct trackDb *tdb) { char geneName[64]; char accName[64]; char sprotName[64]; char posName[64]; char cModeStr[64]; boolean useGene, useAcc, useSprot, usePos; int cMode; char *cModes[3] = {"0", "1", "2"}; safef(geneName, sizeof(geneName), "%s.geneLabel", tdb->track); safef(accName, sizeof(accName), "%s.accLabel", tdb->track); safef(sprotName, sizeof(sprotName), "%s.sprotLabel", tdb->track); safef(posName, sizeof(posName), "%s.posLabel", tdb->track); useGene= cartUsualBoolean(cart, geneName, TRUE); useAcc= cartUsualBoolean(cart, accName, FALSE); useSprot= cartUsualBoolean(cart, sprotName, FALSE); usePos= cartUsualBoolean(cart, posName, FALSE); safef(cModeStr, sizeof(cModeStr), "%s.cmode", tdb->track); cMode = cartUsualInt(cart, cModeStr, 0); printf("
Color elements: "); cgiMakeRadioButton(cModeStr, cModes[0], cMode == 0); printf("by score "); cgiMakeRadioButton(cModeStr, cModes[1], cMode == 1); printf("by human chromosome "); cgiMakeRadioButton(cModeStr, cModes[2], cMode == 2); printf("black"); printf("
Label elements by: ");
cgiMakeCheckBox(geneName, useGene);
printf("Human Gene ");
cgiMakeCheckBox(accName, useAcc);
printf("Human mRNA ");
cgiMakeCheckBox(sprotName, useSprot);
printf("UniProt(Swiss-Prot/TrEMBL) ID ");
cgiMakeCheckBox(posName, usePos);
printf("Human Position");
baseColorDrawOptDropDown(cart, tdb);
}
void hg17KgIdConfig(struct trackDb *tdb)
/* Put up gene ID track controls */
{
char varName[64];
char *geneLabel;
safef(varName, sizeof(varName), "%s.label", tdb->track);
geneLabel = cartUsualString(cart, varName, "gene symbol");
printf("Label: ");
radioButton(varName, geneLabel, "gene symbol");
radioButton(varName, geneLabel, "UCSC Known Gene ID");
radioButton(varName, geneLabel, "all");
radioButton(varName, geneLabel, "none");
}
void hg17KgUI(struct trackDb *tdb)
/* Put up refGene-specific controls */
{
hg17KgIdConfig(tdb);
baseColorDrawOptDropDown(cart, tdb);
}
void omimLocationConfig(struct trackDb *tdb)
/* Put up OMIM Location track controls */
{
char varName[64];
char *geneLabel;
safef(varName, sizeof(varName), "%s.label", tdb->track);
geneLabel = cartUsualString(cart, varName, "OMIM ID");
printf("
Include Entries of: ");
printf("
- \n");
printf("
- "); labelMakeCheckBox(tdb, "class1", "Phenotype map key 1: the disorder has been placed on the map based on its association with a gene, but the underlying defect is not known.", TRUE); printf("
- "); labelMakeCheckBox(tdb, "class2", "Phenotype map key 2: the disorder has been placed on the map by linkage; no mutation has been found.", TRUE); printf("
- "); labelMakeCheckBox(tdb, "class3", "Phenotype map key 3: the molecular basis for the disorder is known; a mutation has been found in the gene.", TRUE); printf("
- "); labelMakeCheckBox(tdb, "class4", "Phenotype map key 4: a contiguous gene deletion or duplication syndrome; multiple genes are deleted or duplicated causing the phenotype.", TRUE); // removed the "others" option for the time being //printf("
- "); //labelMakeCheckBox(tdb, "others", "Others: no associated OMIM phenotype map key info available.", TRUE); printf("
Include Entries of: "); printf("
- \n");
printf("
- "); labelMakeCheckBox(tdb, "class1", "Phenotype map key 1: the disorder has been placed on the map based on its association with a gene, but the underlying defect is not known.", TRUE); printf("
- "); labelMakeCheckBox(tdb, "class2", "Phenotype map key 2: the disorder has been placed on the map by linkage; no mutation has been found.", TRUE); printf("
- "); labelMakeCheckBox(tdb, "class3", "Phenotype map key 3: the molecular basis for the disorder is known; a mutation has been found in the gene.", TRUE); printf("
- "); labelMakeCheckBox(tdb, "class4", "Phenotype map key 4: a contiguous gene deletion or duplication syndrome; multiple genes are deleted or duplicated causing the phenotype.", TRUE); printf("
- "); labelMakeCheckBox(tdb, "others", "Others: no associated OMIM phenotype map key info available.", TRUE); printf("
Label: "); radioButton(varName, geneLabel, "OMIM ID"); radioButton(varName, geneLabel, "OMIM gene or syndrome"); radioButton(varName, geneLabel, "UCSC gene symbol"); } void knownGeneIdConfig(struct trackDb *tdb) /* Put up gene ID track controls */ { struct sqlConnection *conn = hAllocConn(database); char query[256]; char *omimAvail = NULL; safef(query, sizeof(query), "select kgXref.kgID from kgXref,refLink where kgXref.refseq = refLink.mrnaAcc and refLink.omimId != 0 limit 1"); omimAvail = sqlQuickString(conn, query); hFreeConn(&conn); printf("Label: "); labelMakeCheckBox(tdb, "gene", "gene symbol", FALSE); labelMakeCheckBox(tdb, "kgId", "UCSC Known Gene ID", FALSE); labelMakeCheckBox(tdb, "prot", "UniProt Display ID", FALSE); if (omimAvail != NULL) { char sym[32]; safef(sym, sizeof(sym), "omim%s", cartString(cart, "db")); labelMakeCheckBox(tdb, sym, "OMIM ID", FALSE); } printf("
\n"); } void knownGeneShowWhatUi(struct trackDb *tdb) /* Put up line of controls that describe what parts to show. */ { char varName[64]; printf("Show: "); safef(varName, sizeof(varName), "%s.show.noncoding", tdb->track); boolean option = cartUsualBoolean(cart, varName, TRUE); cgiMakeCheckBox(varName, option); printf(" %s ", "non-coding genes"); safef(varName, sizeof(varName), "%s.show.spliceVariants", tdb->track); option = cartUsualBoolean(cart, varName, TRUE); cgiMakeCheckBox(varName, option); printf(" %s ", "splice variants"); printf("
\n"); } void knownGeneUI(struct trackDb *tdb) /* Put up refGene-specific controls */ { /* This is incompatible with adding Protein ID to lf->extra */ knownGeneIdConfig(tdb); knownGeneShowWhatUi(tdb); baseColorDrawOptDropDown(cart, tdb); } void omimLocationUI(struct trackDb *tdb) /* Put up omimLcation-specific controls */ { omimLocationConfig(tdb); } void omimGene2IdConfig(struct trackDb *tdb) /* Put up gene ID track controls */ { printf("Label: "); labelMakeCheckBox(tdb, "omimId", "OMIM ID", FALSE); labelMakeCheckBox(tdb, "gene", "gene symbol", FALSE); printf("
\n"); } void omimGene2UI(struct trackDb *tdb) /* Put up omimGene2-specific controls */ { omimGene2IdConfig(tdb); omimGene2Config(tdb); } void omimGeneUI(struct trackDb *tdb) /* Put up omimGene-specific controls */ { omimGeneIdConfig(tdb); } void geneIdConfig(struct trackDb *tdb) /* Put up gene ID track controls */ { char varName[64]; char *geneLabel; safef(varName, sizeof(varName), "%s.label", tdb->track); geneLabel = cartUsualString(cart, varName, "gene"); printf("Label: "); radioButton(varName, geneLabel, "gene"); radioButton(varName, geneLabel, "accession"); radioButton(varName, geneLabel, "both"); radioButton(varName, geneLabel, "none"); } static void hideNoncodingOpt(struct trackDb *tdb) /* Put up hide-noncoding options. */ { /* Put up option to hide non-coding elements. */ printf("Hide non-coding genes: "); char varName[64]; safef(varName, sizeof(varName), "%s.%s", tdb->track, HIDE_NONCODING_SUFFIX); cartMakeCheckBox(cart, varName, HIDE_NONCODING_DEFAULT); } void rgdGene2UI(struct trackDb *tdb) /* Put up rgdGene2 gene ID track controls, with checkboxes */ { /* Put up label line - boxes for gene and accession. */ printf("Label: "); labelMakeCheckBox(tdb, "gene", "gene", FALSE); labelMakeCheckBox(tdb, "acc", "accession", FALSE); printf("
\n"); baseColorDrawOptDropDown(cart, tdb); } void refGeneUI(struct trackDb *tdb) /* Put up refGene or xenoRefGene gene ID track controls, with checkboxes */ { /* Figure out if OMIM database is available. */ int omimAvail = 0; if (sameString(tdb->track, "refGene")) { struct sqlConnection *conn = hAllocConn(database); char query[128]; safef(query, sizeof(query), "select refLink.omimId from refLink, refGene where refLink.mrnaAcc = refGene.name and refLink.omimId != 0 limit 1"); omimAvail = sqlQuickNum(conn, query); hFreeConn(&conn); } /* Put up label line - boxes for gene, accession or maybe OMIM. */ printf("Label: "); -labelMakeCheckBox(tdb, "gene", "gene", FALSE); +labelMakeCheckBox(tdb, "gene", "gene", TRUE); labelMakeCheckBox(tdb, "acc", "accession", FALSE); if (omimAvail != 0) { char sym[32]; safef(sym, sizeof(sym), "omim%s", cartString(cart, "db")); labelMakeCheckBox(tdb, sym, "OMIM ID", FALSE); } printf("
\n"); /* Put up noncoding option and codon coloring stuff. */ hideNoncodingOpt(tdb); baseColorDrawOptDropDown(cart, tdb); } void transMapUI(struct trackDb *tdb) /* Put up transMap-specific controls */ { printf("Label: "); labelMakeCheckBox(tdb, "orgCommon", "common name", FALSE); labelMakeCheckBox(tdb, "orgAbbrv", "organism abbreviation", FALSE); labelMakeCheckBox(tdb, "db", "assembly database", FALSE); labelMakeCheckBox(tdb, "gene", "gene", FALSE); labelMakeCheckBox(tdb, "acc", "accession", FALSE); baseColorDrawOptDropDown(cart, tdb); indelShowOptions(cart, tdb); } void retroGeneUI(struct trackDb *tdb) /* Put up retroGene-specific controls */ { printf("Label: "); labelMakeCheckBox(tdb, "gene", "gene", FALSE); labelMakeCheckBox(tdb, "acc", "accession", FALSE); baseColorDrawOptDropDown(cart, tdb); } void vegaGeneUI(struct trackDb *tdb) /* Put up Vega Gene track-specific controls */ { geneIdConfig(tdb); printf("
\n"); /* Put up codon coloring stuff. */ baseColorDrawOptDropDown(cart, tdb); } void ensemblNonCodingTypeConfig(struct trackDb *tdb) { int i = 0; printf("
Non-coding RNA type: "); printf("
\n"); for (i=0; i < nonCodingTypeLabelsSize; i++) { nonCodingTypeIncludeCart[i] = cartUsualBoolean(cart, nonCodingTypeIncludeStrings[i], nonCodingTypeIncludeDefault[i]); cgiMakeCheckBox(nonCodingTypeIncludeStrings[i], nonCodingTypeIncludeCart[i]); printf(" %s", nonCodingTypeLabels[i]); } } void ensemblNonCodingUI(struct trackDb *tdb) /* Put up Ensembl Non-Coding genes-specific controls */ { ensemblNonCodingTypeConfig(tdb); } void transRegCodeUi(struct trackDb *tdb) /* Put up UI for transcriptional regulatory code - not * much more than score UI. */ { printf("%s", "
The scoring ranges from 0 to 1000 and is based on the number of lines " "of evidence that support the motif being active. Each of the two " "sensu stricto species in which the motif was conserved counts " "as a line of evidence. If the ChIP-chip data showed good (P ≤ 0.001) " "evidence of binding to the transcription factor associated with the " "motif, that counts as two lines of evidence. If the ChIP-chip data " "showed weaker (P ≤ 0.005) evidence of binding, that counts as just one line " "of evidence. The following table shows the relationship between lines " "of evidence and score:"); printf("
"); hTableStart(); printf("%s", "
\n" "\n" ); hTableEnd(); } void zooWiggleUi(struct trackDb *tdb ) /* put up UI for zoo track with one species on each line * and checkboxes to toggle each of them on/off*/ { char options[7][256]; int thisHeightPer, thisLineGap; float thisMinYRange, thisMaxYRange; char *interpolate, *fill; char **row; int rowOffset; struct sample *sample; struct sqlResult *sr; char option[64]; struct sqlConnection *conn = hAllocConn(database); char newRow = 0; snprintf( &options[0][0], 256, "%s.heightPer", tdb->track ); snprintf( &options[1][0], 256, "%s.linear.interp", tdb->track ); snprintf( &options[3][0], 256, "%s.fill", tdb->track ); snprintf( &options[4][0], 256, "%s.min.cutoff", tdb->track ); snprintf( &options[5][0], 256, "%s.max.cutoff", tdb->track ); snprintf( &options[6][0], 256, "%s.interp.gap", tdb->track ); thisHeightPer = atoi(cartUsualString(cart, &options[0][0], "50")); interpolate = cartUsualString(cart, &options[1][0], "Linear Interpolation"); fill = cartUsualString(cart, &options[3][0], "1"); thisMinYRange = atof(cartUsualString(cart, &options[4][0], "0.0")); thisMaxYRange = atof(cartUsualString(cart, &options[5][0], "1000.0")); thisLineGap = atoi(cartUsualString(cart, &options[6][0], "200")); printf("\n" " Evidence Score \n" " 4 1000 \n" " 3 500 \n" " 2 333 \n" " 1 250 \n" " 0 200
Interpolation: ");
wiggleDropDown(&options[1][0], interpolate );
printf(" ");
printf("
");
printf(" Fill Blocks: ");
cgiMakeRadioButton(&options[3][0], "1", sameString(fill, "1"));
printf(" on ");
cgiMakeRadioButton(&options[3][0], "0", sameString(fill, "0"));
printf(" off ");
printf("
Track Height: "); cgiMakeIntVar(&options[0][0], thisHeightPer, 5 ); printf(" pixels"); printf("
Vertical Range: \nmin:"); cgiMakeDoubleVar(&options[4][0], thisMinYRange, 6 ); printf(" max:"); cgiMakeDoubleVar(&options[5][0], thisMaxYRange, 6 ); printf("
Toggle Species on/off
" );
sr = hRangeQuery(conn, tdb->table, chromosome, 0, 1877426, NULL, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
sample = sampleLoad(row + rowOffset);
snprintf( option, sizeof(option), "zooSpecies.%s", sample->name );
if( cartUsualBoolean(cart, option, TRUE ) )
cgiMakeCheckBox(option, TRUE );
else
cgiMakeCheckBox(option, FALSE );
printf("%s ", sample->name );
newRow++;
if( newRow % 5 == 0 ) printf("
");
sampleFree(&sample);
}
}
void chainColorUi(struct trackDb *tdb)
/* UI for the chain tracks */
{
boolean normScoreAvailable = chainDbNormScoreAvailable(tdb);
boolean compositeTrack = tdbIsComposite(tdb);
if (compositeTrack)
return; // configuration taken care of by hCompositeUi() later
else if (normScoreAvailable)
chainCfgUi(database, cart, tdb, tdb->track, NULL, FALSE, chromosome);
else
crossSpeciesCfgUi(cart,tdb);
}
void chromGraphUi(struct trackDb *tdb)
/* UI for the wiggle track */
{
char varName[chromGraphVarNameMaxSize];
struct sqlConnection *conn = NULL;
char *track = tdb->track;
if (!isCustomTrack(track))
conn = hAllocConn(database);
double minVal,maxVal;
struct chromGraphSettings *cgs = chromGraphSettingsGet(track,
conn, tdb, cart);
printf("Track height: ");
chromGraphVarName(track, "pixels", varName);
cgiMakeIntVar(varName, cgs->pixels, 3);
printf(" pixels (range: %d to %d)
",
cgs->minPixels, cgs->maxPixels);
printf("Vertical viewing range: \nmin: ");
chromGraphVarName(track, "minVal", varName);
cgiMakeDoubleVar(varName, cgs->minVal, 6);
printf(" max: ");
chromGraphVarName(track, "maxVal", varName);
cgiMakeDoubleVar(varName, cgs->maxVal, 6);
if (conn)
chromGraphDataRange(track, conn, &minVal, &maxVal);
else
{
char *fileName = trackDbRequiredSetting(tdb, "binaryFile");
struct chromGraphBin *cgb = chromGraphBinOpen(fileName);
minVal = cgb->minVal;
maxVal = cgb->maxVal;
chromGraphBinFree(&cgb);
}
printf("\n (range: %g to %g)
",
minVal, maxVal);
hFreeConn(&conn);
}
void wikiTrackUi(struct trackDb *tdb)
/* UI for wiki track user annotations */
{
return; // currently empty
}
void rulerUi(struct trackDb *tdb)
/* UI for base position (ruler) */
{
boolean showScaleBar = cartUsualBoolean(cart, BASE_SCALE_BAR, TRUE);
boolean showRuler = cartUsualBoolean(cart, BASE_SHOWRULER, TRUE);
boolean complementsToo = cartUsualBoolean(cart, MOTIF_COMPLEMENT, FALSE);
boolean showPos = cartUsualBoolean(cart, BASE_SHOWPOS, FALSE);
boolean showAsm = cartUsualBoolean(cart, BASE_SHOWASM, FALSE);
/* title var is assembly-specific */
char titleVar[256];
char *title = NULL;
/* Configure zoom when click occurs */
char *currentZoom = cartCgiUsualString(cart, RULER_BASE_ZOOM_VAR, ZOOM_3X);
char *motifString = cartCgiUsualString(cart, BASE_MOTIFS, "");
safef(titleVar,sizeof(titleVar),"%s_%s",BASE_TITLE,database);
title = cartUsualString(cart, titleVar, "");
puts("
"); cgiMakeCheckBox(BASE_SHOWRULER, showRuler); puts(" Show ruler
"); puts(""); cgiMakeCheckBox(BASE_SCALE_BAR, showScaleBar); puts(" Show scale bar"); puts("
"); cgiMakeCheckBox(BASE_SHOWASM_SCALEBAR, cartUsualBoolean(cart, BASE_SHOWASM_SCALEBAR, TRUE)); puts(" Show assembly next to scale bar"); puts("
"); puts("Zoom factor: "); zoomRadioButtons(RULER_BASE_ZOOM_VAR, currentZoom); puts("
Motifs to highlight: "); cgiMakeTextVar(BASE_MOTIFS, motifString, 20); puts(" (Comma separated list, i.e.: GT,AG for splice sites)"); puts("
"); cgiMakeCheckBox(MOTIF_COMPLEMENT, complementsToo); puts(" Show reverse complements of motifs also"); puts("
Options for slides and presentations:"); puts("
Title: "); cgiMakeTextVar(titleVar, title, 30); puts("
Display: "); cgiMakeCheckBox(BASE_SHOWASM, showAsm); puts(" assembly "); cgiMakeCheckBox(BASE_SHOWPOS, showPos); puts(" position"); } void pubsUi(struct trackDb *tdb) /* UI for pubs match track */ { #define NUM_YEARS 30 // similar to google scholar, which goes back to 20 years #define PUBS_KEYWORDS_TAG "pubsKeywords" #define PUBS_YEAR_TAG "pubsYear" // get current set filters from cart char *keywords = cartUsualStringClosestToHome(cart, tdb, FALSE, PUBS_KEYWORDS_TAG, ""); char *yearFilter = cartUsualStringClosestToHome(cart, tdb, FALSE, PUBS_YEAR_TAG, "anytime"); // print keyword input box puts("
Filter articles by keywords in abstract, title or authors:");
char cgiVar[128];
safef(cgiVar,sizeof(cgiVar),"%s.%s",tdb->track,PUBS_KEYWORDS_TAG);
cgiMakeTextVar(cgiVar, keywords, 45);
// generate strings like "since
\n"); printf("Show articles published "); safef(cgiVar,sizeof(cgiVar),"%s.%s",tdb->track,PUBS_YEAR_TAG); cgiDropDownWithTextValsAndExtra(cgiVar, text, values, NUM_YEARS + 1, yearFilter, NULL); puts("
\n"); } void oligoMatchUi(struct trackDb *tdb) /* UI for oligo match track */ { char *oligo = cartUsualString(cart, oligoMatchVar, oligoMatchDefault); puts("Short (2-30 base) sequence:"); cgiMakeTextVar(oligoMatchVar, oligo, 45); } void cutterUi(struct trackDb *tdb) /* UI for restriction enzyme track */ { char *enz = cartUsualString(cart, cutterVar, cutterDefault); puts("
Filter display by enzymes (separate with commas):
");
cgiMakeTextVar(cutterVar, enz, 100);
}
void genericWiggleUi(struct trackDb *tdb, int optionNum )
/* put up UI for any standard wiggle track (a.k.a. sample track)*/
{
char options[7][256];
int thisHeightPer, thisLineGap;
float thisMinYRange, thisMaxYRange;
char *interpolate, *fill;
snprintf( &options[0][0], 256, "%s.heightPer", tdb->track );
snprintf( &options[1][0], 256, "%s.linear.interp", tdb->track );
snprintf( &options[3][0], 256, "%s.fill", tdb->track );
snprintf( &options[4][0], 256, "%s.min.cutoff", tdb->track );
snprintf( &options[5][0], 256, "%s.max.cutoff", tdb->track );
snprintf( &options[6][0], 256, "%s.interp.gap", tdb->track );
thisHeightPer = atoi(cartUsualString(cart, &options[0][0], "50"));
interpolate = cartUsualString(cart, &options[1][0], "Linear Interpolation");
fill = cartUsualString(cart, &options[3][0], "1");
thisMinYRange = atof(cartUsualString(cart, &options[4][0], "0.0"));
thisMaxYRange = atof(cartUsualString(cart, &options[5][0], "1000.0"));
thisLineGap = atoi(cartUsualString(cart, &options[6][0], "200"));
printf("
Interpolation: ");
wiggleDropDown(&options[1][0], interpolate );
printf(" ");
printf("
");
printf(" Fill Blocks: ");
cgiMakeRadioButton(&options[3][0], "1", sameString(fill, "1"));
printf(" on ");
cgiMakeRadioButton(&options[3][0], "0", sameString(fill, "0"));
printf(" off ");
printf("
Track Height: "); cgiMakeIntVar(&options[0][0], thisHeightPer, 5 ); printf(" pixels"); printf("
Vertical Range: \nmin:"); cgiMakeDoubleVar(&options[4][0], thisMinYRange, 6 ); printf(" max:"); cgiMakeDoubleVar(&options[5][0], thisMaxYRange, 6 ); if( optionNum >= 7 ) { printf("
Maximum Interval to Interpolate Across: "); cgiMakeIntVar(&options[6][0], thisLineGap, 10 ); printf(" bases"); } } void affyTxnPhase2Ui(struct trackDb *tdb) /* Ui for affymetrix transcriptome phase 2 data. */ { enum trackVisibility tnfgVis = tvHide; char *visString = cartUsualString(cart, "hgt.affyPhase2.tnfg", "hide"); tnfgVis = hTvFromString(visString); printf("Transfrags Display Mode: "); hTvDropDown("hgt.affyPhase2.tnfg", tnfgVis, TRUE); wigCfgUi(cart,tdb,tdb->track,"Graph Plotting options:",FALSE); printf("
View/Hide individual cell lines:"); } void humMusUi(struct trackDb *tdb, int optionNum ) /* put up UI for human/mouse conservation sample tracks (humMusL and musHumL)*/ { char options[7][256]; int thisHeightPer, thisLineGap; float thisMinYRange, thisMaxYRange; char *interpolate, *fill; snprintf( &options[0][0], 256, "%s.heightPer", tdb->track ); snprintf( &options[1][0], 256, "%s.linear.interp", tdb->track ); snprintf( &options[3][0], 256, "%s.fill", tdb->track ); snprintf( &options[4][0], 256, "%s.min.cutoff", tdb->track ); snprintf( &options[5][0], 256, "%s.max.cutoff", tdb->track ); snprintf( &options[6][0], 256, "%s.interp.gap", tdb->track ); thisHeightPer = atoi(cartUsualString(cart, &options[0][0], "50")); interpolate = cartUsualString(cart, &options[1][0], "Linear Interpolation"); fill = cartUsualString(cart, &options[3][0], "1"); thisMinYRange = atof(cartUsualString(cart, &options[4][0], "0.0")); thisMaxYRange = atof(cartUsualString(cart, &options[5][0], "8.0")); thisLineGap = atoi(cartUsualString(cart, &options[6][0], "200")); printf("
Interpolation: ");
wiggleDropDown(&options[1][0], interpolate );
printf(" ");
printf("
");
printf(" Fill Blocks: ");
cgiMakeRadioButton(&options[3][0], "1", sameString(fill, "1"));
printf(" on ");
cgiMakeRadioButton(&options[3][0], "0", sameString(fill, "0"));
printf(" off ");
printf("
Track Height: "); cgiMakeIntVar(&options[0][0], thisHeightPer, 5 ); printf(" pixels"); printf("
Vertical Range: \nmin:"); cgiMakeDoubleVar(&options[4][0], thisMinYRange, 6 ); printf(" max:"); cgiMakeDoubleVar(&options[5][0], thisMaxYRange, 6 ); if( optionNum >= 7 ) { printf("
Maximum Interval to Interpolate Across: ");
cgiMakeIntVar(&options[6][0], thisLineGap, 10 );
printf(" bases");
}
}
void affyTranscriptomeUi(struct trackDb *tdb)
/* put up UI for the GC percent track (a sample track)*/
{
int affyTranscriptomeHeightPer = atoi(cartUsualString(cart, "affyTranscriptome.heightPer", "100"));
char *fill = cartUsualString(cart, "affyTranscriptome.fill", "1");
printf("
");
printf(" Fill Blocks: ");
cgiMakeRadioButton("affyTranscriptome.fill", "1", sameString(fill, "1"));
printf(" on ");
cgiMakeRadioButton("affyTranscriptome.fill", "0", sameString(fill, "0"));
printf(" off ");
printf("
Track Height: "); cgiMakeIntVar("affyTranscriptome.heightPer", affyTranscriptomeHeightPer, 5 ); printf(" pixels"); } void ancientRUi(struct trackDb *tdb) /* put up UI for the ancient repeats track to let user enter an * integer to filter out those repeats with less aligned bases.*/ { int ancientRMinLength = atoi(cartUsualString(cart, "ancientR.minLength", "50")); printf("
Length Filter
Exclude aligned repeats with less than ");
cgiMakeIntVar("ancientR.minLength", ancientRMinLength, 4 );
printf("aligned bases (not necessarily identical). Enter 0 for no filtering.");
}
void affyTransfragUi(struct trackDb *tdb)
/* Options for filtering affymetrix transfrag track based on score. */
{
boolean skipPseudos = cartUsualBoolean(cart, "affyTransfrags.skipPseudos", TRUE);
boolean skipDups = cartUsualBoolean(cart, "affyTransfrags.skipDups", FALSE);
printf("
");
cgiMakeCheckBox("affyTransfrags.skipPseudos", skipPseudos);
printf(" Remove transfrags that overlap pseudogenes from display.
");
cgiMakeCheckBox("affyTransfrags.skipDups", skipDups);
printf(" Remove transfrags that have a BLAT match elsewhere in the genome from display.
");
}
void ucsfdemoUi(struct trackDb *tdb)
{
char **menu;
int menuSize = 0;
int menuPos = 0;
puts("
ER filter: ");
menuSize = 3;
menu = needMem((size_t)(menuSize * sizeof(char *)));
menuPos = 0;
menu[menuPos++] = "no filter";
menu[menuPos++] = "pos";
menu[menuPos++] = "neg";
cgiMakeDropList(UCSF_DEMO_ER, menu, menuSize,
cartCgiUsualString(cart, UCSF_DEMO_ER, UCSF_DEMO_ER_DEFAULT));
freez(&menu);
puts("
PR filter: ");
menuSize = 3;
menu = needMem((size_t)(menuSize * sizeof(char *)));
menuPos = 0;
menu[menuPos++] = "no filter";
menu[menuPos++] = "pos";
menu[menuPos++] = "neg";
cgiMakeDropList(UCSF_DEMO_PR, menu, menuSize,
cartCgiUsualString(cart, UCSF_DEMO_PR, UCSF_DEMO_PR_DEFAULT));
freez(&menu);
}
void hapmapSnpsUi(struct trackDb *tdb)
/* Options for filtering hapmap snps */
/* Default is always to not filter (include all data) */
/* snp track puts the menu options in kent/src/hg/lib/snp125Ui.h */
/* snp track also sets global variables, don't actually need this? */
/* Consider using radio buttons */
{
struct sqlConnection *conn = hAllocConn(database);
boolean isPhaseIII = sameString(trackDbSettingOrDefault(tdb, "hapmapPhase", "II"), "III");
if ((isPhaseIII && !sqlTableExists(conn, "hapmapPhaseIIISummary")) ||
(!isPhaseIII & !sqlTableExists(conn, "hapmapAllelesSummary")))
return;
puts("
");
puts("Display filters (applied to all subtracks):");
puts("
\n");
puts("
Population availability: ");
static char *popAvailMenuPhaseIII[] =
{ "no filter",
"all 11 Phase III populations",
"all 4 Phase II populations" };
static char *popAvailMenuPhaseII[] =
{ "no filter",
"all 4 populations",
"1-3 populations" };
char **menu = isPhaseIII ? popAvailMenuPhaseIII : popAvailMenuPhaseII;
cgiMakeDropList(HAP_POP_COUNT, menu, 3,
cartUsualString(cart, HAP_POP_COUNT, HAP_FILTER_DEFAULT));
puts("
Major allele mixture between populations: ");
static char *mixedMenu[] = { "no filter", "mixed", "not mixed" };
cgiMakeDropList(HAP_POP_MIXED, mixedMenu, 3,
cartUsualString(cart, HAP_POP_MIXED, HAP_FILTER_DEFAULT));
puts("
Monomorphism:
");
static char *noYesNoMenu[] = { "no filter", "yes", "no" };
char **pops = isPhaseIII ? hapmapPhaseIIIPops : hapmapPhaseIIPops;
int popCount = isPhaseIII ? HAP_PHASEIII_POPCOUNT : HAP_PHASEII_POPCOUNT;
puts("
| %s: | ", pops[i]); safef(cartVar, sizeof(cartVar), "%s_%s", HAP_MONO_PREFIX, pops[i]); cgiMakeDropList(cartVar, noYesNoMenu, 3, cartUsualString(cart, cartVar, HAP_FILTER_DEFAULT)); printf(" | \n"); cellCount += 2; if (cellCount == 12) { puts(""); puts(""); } puts(" |
Polymorphism type: "); static char *typeMenu[] = { "no filter", "bi-allelic", "transition", "transversion", "complex" }; cgiMakeDropList(HAP_TYPE, typeMenu, 5, cartUsualString(cart, HAP_TYPE, HAP_FILTER_DEFAULT)); puts("
Minor allele frequency in any population: min: "); float minFreq = atof(cartUsualString(cart, HAP_MIN_FREQ, HAP_MIN_FREQ_DEFAULT)); cgiMakeDoubleVar(HAP_MIN_FREQ, minFreq, 6); puts("max: "); float maxFreq = atof(cartUsualString(cart, HAP_MAX_FREQ, HAP_MAX_FREQ_DEFAULT)); cgiMakeDoubleVar(HAP_MAX_FREQ, maxFreq, 6); puts(" (range: 0.0 to 0.5)\n"); if (isPhaseIII) puts("
Average of populations' observed heterozygosities: "); else puts("
Expected heterozygosity (from total allele frequencies): "); puts("min: "); float minHet = atof(cartUsualString(cart, HAP_MIN_HET, HAP_MIN_HET_DEFAULT)); cgiMakeDoubleVar(HAP_MIN_HET, minHet, 6); puts("max: "); if (isPhaseIII) { float maxHet = atof(cartUsualString(cart, HAP_MAX_OBSERVED_HET, HAP_MAX_OBSERVED_HET_DEFAULT)); cgiMakeDoubleVar(HAP_MAX_OBSERVED_HET, maxHet, 6); puts(" (range: 0.0 to 1.0)\n"); } else { float maxHet = atof(cartUsualString(cart, HAP_MAX_EXPECTED_HET, HAP_MAX_EXPECTED_HET_DEFAULT)); cgiMakeDoubleVar(HAP_MAX_EXPECTED_HET, maxHet, 6); puts(" (range: 0.0 to 0.5)\n"); } static char *orthoMenu[] = { "no filter", "available", "matches major human allele", "matches minor human allele", "matches neither human allele" }; puts("
| %s allele: | \n", hapmapOrthoSpecies[i]); safef(cartVar, sizeof(cartVar), "%s_%s", HAP_ORTHO_PREFIX, hapmapOrthoSpecies[i]); cgiMakeDropList(cartVar, orthoMenu, 5, cartUsualString(cart, cartVar, HAP_FILTER_DEFAULT)); puts(" | "); safef(cartVar, sizeof(cartVar), "%s_%s", HAP_ORTHO_QUAL_PREFIX, hapmapOrthoSpecies[i]); int minQual = atoi(cartUsualString(cart, cartVar, HAP_ORTHO_QUAL_DEFAULT)); puts("Minimum quality score: | \n"); cgiMakeIntVar(cartVar, minQual, 4); puts(" (range: 0 to 100) |
\n"); hFreeConn(&conn); } void pcrResultUi(struct trackDb *tdb) /* Result from hgPcr query. */ { struct targetDb *target; if (! pcrResultParseCart(database, cart, NULL, NULL, &target)) return; if (target != NULL) { char *chosen = cartUsualString(cart, PCR_RESULT_TARGET_STYLE, PCR_RESULT_TARGET_STYLE_DEFAULT); cgiMakeRadioButton(PCR_RESULT_TARGET_STYLE, PCR_RESULT_TARGET_STYLE_TRIM, sameString(chosen, PCR_RESULT_TARGET_STYLE_TRIM)); printf("Show only the amplified part of %s item \n", target->description); cgiMakeRadioButton(PCR_RESULT_TARGET_STYLE, PCR_RESULT_TARGET_STYLE_TALL, sameString(chosen, PCR_RESULT_TARGET_STYLE_TALL)); printf("Show the whole %s item with amplified part tall", target->description); } baseColorDrawOptDropDown(cart, tdb); } void dgvUi(struct trackDb *tdb) /* Database of Genomic Variants: filter by publication. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; safef(query, sizeof(query), "select reference,pubMedId from %s group by pubMedId order by reference;", tdb->table); sr = sqlGetResult(conn, query); printf("
Filter by publication reference:\n"); char cartVarName[256]; safef (cartVarName, sizeof(cartVarName), "hgt_%s_filterType", tdb->track); boolean isInclude = sameString("include", cartUsualString(cart, cartVarName, "include")); cgiMakeRadioButton(cartVarName, "include", isInclude); printf("include\n"); cgiMakeRadioButton(cartVarName, "exclude", !isInclude); printf("exclude
\n"); safef (cartVarName, sizeof(cartVarName), "hgt_%s_filterPmId", tdb->track); boolean filterPmIdInCart = cartListVarExists(cart, cartVarName); struct slName *checked = NULL; if (filterPmIdInCart) checked = cartOptionalSlNameList(cart, cartVarName); #define MAX_DGV_REFS 128 char *labelArr[MAX_DGV_REFS], *valueArr[MAX_DGV_REFS]; int refCount = 0; while ((row = sqlNextRow(sr)) != NULL) { char *ref = row[0]; char *pmId = row[1]; char label[512]; safef(label, sizeof(label), "%s", pmId, ref); labelArr[refCount] = cloneString(label); valueArr[refCount++] = cloneString(pmId); if (! filterPmIdInCart) slNameAddHead(&checked, pmId); if (refCount >= MAX_DGV_REFS) errAbort("dgvUi: %s has too many references (max %d)", tdb->track, MAX_DGV_REFS); } sqlFreeResult(&sr); jsMakeCheckboxGroupSetClearButton(cartVarName, TRUE); jsMakeCheckboxGroupSetClearButton(cartVarName, FALSE); cgiMakeCheckboxGroupWithVals(cartVarName, labelArr, valueArr, refCount, checked, 4); hFreeConn(&conn); } static void factorSourceUi(char *db,struct trackDb *tdb) { printf("
Cell Abbreviations:
\n"); char *sourceTable = trackDbRequiredSetting(tdb, "sourceTable"); struct sqlConnection *conn = hAllocConn(db); hPrintAbbreviationTable(conn, sourceTable, "Cell Type"); hFreeConn(&conn); } #ifdef UNUSED static boolean isInTrackList(struct trackDb *tdbList, struct trackDb *target) /* Return TRUE if target is in tdbList. */ { struct trackDb *tdb; for (tdb = tdbList; tdb != NULL; tdb = tdb->next) if (tdb == target) return TRUE; return FALSE; } #endif /* UNUSED */ void superTrackUi(struct trackDb *superTdb, struct trackDb *tdbList) /* List tracks in this collection, with visibility controls and UI links */ { #define SUPERS_WITH_CHECKBOXES #ifdef SUPERS_WITH_CHECKBOXES #ifdef BUTTONS_BY_CSS #define BUTTON_SUPER "%c" #define BUTTON_PLUS_SUPER() printf(BUTTON_SUPER,"true", '+') #define BUTTON_MINUS_SUPER() printf(BUTTON_SUPER,"false",'-') #else///ifndef BUTTONS_BY_CSS #define PM_BUTTON_GLOBAL "
"
#define BUTTON_PLUS_SUPER() printf(PM_BUTTON_GLOBAL,"true", "plus_all", "add_sm.gif")
#define BUTTON_MINUS_SUPER() printf(PM_BUTTON_GLOBAL,"false","minus_all","remove_sm.gif")
#endif///ndef BUTTONS_BY_CSS
jsIncludeFile("hui.js",NULL);
#endif///def SUPERS_WITH_CHECKBOXES
printf("\n| ");
BUTTON_PLUS_SUPER();
BUTTON_MINUS_SUPER();
printf(" All "); printf(" | ||
| "); if (!tdbIsDownloadsOnly(tdb)) { enum trackVisibility tv = hTvFromString(cartUsualString(cart, tdb->track,hStringFromTv(tdb->visibility))); // Don't use cheapCgi code... no name and no boolshad... just js printf("",tdb->track,(tv != tvHide?" CHECKED":"")); hTvDropDownClassVisOnlyAndExtra(tdb->track, tv, tdb->canPack, (tv == tvHide ? "hiddenText":"normalText"), trackDbSetting(tdb, "onlyVisibility"), "onchange='superT.selChanged(this);'"); printf(" | \n"); printf("%s ", (tdbIsDownloadsOnly(tdb)? hgFileUiName(): hgTrackUiName()), cartSessionVarName(), cartSessionId(cart), chromosome, cgiEncode(tdb->track), tdb->shortLabel); } else { printf("Downloads", hgFileUiName(),cartSessionVarName(), cartSessionId(cart), cgiEncode(tdb->track)); printf(" | \n"); printf("%s ",tdb->shortLabel); } printf(" | \n"); #else///ifndef SUPERS_WITH_CHECKBOXES printf("
| "); if (tdbIsDownloadsOnly(tdb)) printf("%s ",tdb->shortLabel); else printf("%s ", (tdbIsDownloadsOnly(tdb)? hgFileUiName(): hgTrackUiName()), cartSessionVarName(), cartSessionId(cart), chromosome, cgiEncode(tdb->track), tdb->shortLabel); printf(" | "); if (tdbIsDownloadsOnly(tdb)) { printf("Downloads", hgFileUiName(),cartSessionVarName(), cartSessionId(cart), cgiEncode(tdb->track)); } else { enum trackVisibility tv = hTvFromString(cartUsualString(cart, tdb->track, hStringFromTv(tdb->visibility))); hTvDropDownClassVisOnly(tdb->track, tv, tdb->canPack, tv == tvHide ? "hiddenText" : "normalText", trackDbSetting(tdb, "onlyVisibility")); } #endif///ndef SUPERS_WITH_CHECKBOXES printf(" | %s", tdb->longLabel); char *dataVersion = trackDbSetting(tdb, "dataVersion"); if (dataVersion) printf(" %s", dataVersion); printf(" |
WARNING: This data is provided for early access via the Preview Browser -- it is unreviewed and subject to change. For high quality reviewed annotations, see the Genome Browser.", "genome.ucsc.edu", db); } else { // TODO: use hTrackUiName() printf("
NOTE: Early access to additional track data may be available on the Preview Browser.",
"genome-preview.ucsc.edu", db, tdb->track);
}
}
}
void specificUi(struct trackDb *tdb, struct trackDb *tdbList, struct customTrack *ct, boolean ajax)
/* Draw track specific parts of UI. */
{
char *track = tdb->track;
// Ideally check cfgTypeFromTdb()/cfgByCfgType() first, but with all these special cases already in
// place, lets be cautious at this time.
// NOTE: Developer, please try to use cfgTypeFromTdb()/cfgByCfgType().
boolean boxed = trackDbSettingClosestToHomeOn(tdb, "boxedCfg");
// UI precedence:
// 1) supers to get them out of the way: they have no controls
// 2) special cases based upon track name (developer please avoid)
// 3) cfgTypeFromTdb()/cfgByCfgType() <== prefered method
// 4) special cases falling through the cracks but based upon type
if (tdbIsSuperTrack(tdb))
superTrackUi(tdb, tdbList);
else if (sameString(track, "stsMap"))
stsMapUi(tdb);
else if (sameString(track, "affyTxnPhase2"))
affyTxnPhase2Ui(tdb);
else if (sameString(track, "cgapSage"))
cgapSageUi(tdb);
else if (sameString(track, "stsMapMouseNew"))
stsMapMouseUi(tdb);
else if (sameString(track, "stsMapRat"))
stsMapRatUi(tdb);
else if (sameString(track, "snpMap"))
snpMapUi(tdb);
else if (sameString(track, "snp"))
snpUi(tdb);
else if (snpVersion(track) >= 125)
snp125Ui(tdb);
else if (sameString(track, "rertyHumanDiversityLd")
|| startsWith("hapmapLd", track)
|| sameString(tdb->type, "ld2"))
ldUi(tdb);
else if (sameString(track, "cbr_waba"))
cbrWabaUi(tdb);
else if (sameString(track, "fishClones"))
fishClonesUi(tdb);
else if (sameString(track, "recombRate"))
recombRateUi(tdb);
else if (sameString(track, "recombRateRat"))
recombRateRatUi(tdb);
else if (sameString(track, "recombRateMouse"))
recombRateMouseUi(tdb);
else if (sameString(track, "cghNci60"))
cghNci60Ui(tdb);
else if (sameString(track, "xenoRefGene")
|| sameString(track, "refGene"))
refGeneUI(tdb);
else if (startsWith("transMapAln", track))
transMapUI(tdb);
else if (sameString(track, "rgdGene2"))
rgdGene2UI(tdb);
else if (sameString(track, "knownGene"))
knownGeneUI(tdb);
else if (sameString(track, "omimLocation"))
omimLocationUI(tdb);
else if (sameString(track, "omimGene2"))
omimGene2UI(tdb);
else if (sameString(track, "omimGene"))
omimGeneUI(tdb);
else if (sameString(track, "hg17Kg"))
hg17KgUI(tdb);
else if (startsWith("ucscRetro", track)
|| startsWith("retroMrnaInfo", track))
retroGeneUI(tdb);
else if (sameString(track, "ensGeneNonCoding"))
ensemblNonCodingUI(tdb);
else if (sameString(track, "vegaGeneComposite"))
vegaGeneUI(tdb);
else if (sameString(track, "rosetta"))
rosettaUi(tdb);
else if (startsWith("pubs", track))
pubsUi(tdb);
else if (startsWith("blastDm", track))
blastFBUi(tdb);
else if (sameString(track, "blastSacCer1SG"))
blastSGUi(tdb);
else if (sameString(track, "blastHg17KG")
|| sameString(track, "blastHg16KG")
|| sameString(track, "blastCe3WB")
|| sameString(track, "blastHg18KG")
|| sameString(track, "blatzHg17KG")
|| startsWith("mrnaMap", track)
|| startsWith("mrnaXeno", track))
blastUi(tdb);
else if (sameString(track, "hgPcrResult"))
pcrResultUi(tdb);
else if (sameString(track, "ancientR"))
ancientRUi(tdb);
else if (sameString(track, "zoo")
|| sameString(track, "zooNew" ))
zooWiggleUi(tdb);
else if (sameString(track, "humMusL")
|| sameString(track, "musHumL")
|| sameString(track, "regpotent")
|| sameString(track, "mm3Rn2L" )
|| sameString(track, "mm3Hg15L" )
|| sameString(track, "hg15Mm3L" ))
humMusUi(tdb,7);
else if (startsWith("chain", track)
|| endsWith("chainSelf", track))
chainColorUi(tdb);
else if (sameString(track, "orthoTop4") // still used ??
|| sameString(track, "mouseOrtho")
|| sameString(track, "mouseSyn"))
// NOTE: type psl xeno Retrieved from %s Track...
\n",COLOR_DARKGREEN,tdbParent->shortLabel);
puts(tdbParent->html);
}
else
printf("No description found for: %s.
",tdbParent?tdbParent->track:tdb->track);
}
cartRemove(cart,"descriptionOnly"); // This is a once only request and should be deleted
return;
}
if(tdbIsContainer(tdb))
{
safef(setting,sizeof(setting),"%s.%s",tdb->track,RESET_TO_DEFAULTS);
// NOTE: if you want track vis to not be reset, move to after vis dropdown
if (1 == cartUsualInt(cart, setting, 0))
cartRemoveAllForTdbAndChildren(cart,tdb);
else if (!ajax) // Overkill on !ajax, because ajax shouldn't be called for a composite
cartTdbTreeReshapeIfNeeded(cart,tdb);
}
printf("");
if (ajax)
return;
if (ct)
{
/* hidden form for custom tracks CGI */
printf("\n");
if (ct->bbiFile)
{
time_t timep = bbiUpdateTime(ct->bbiFile);
printBbiUpdateTime(&timep);
}
else
printUpdateTime(CUSTOM_TRASH, ct->tdb, ct);
}
if (!ct)
{
/* Print data version trackDB setting, if any */
struct trackVersion *trackVersion = getTrackVersion(database, tdb->track);
char *version = trackVersion == NULL ? trackDbSetting(tdb, "dataVersion") : trackVersion->version;
if (version)
{
cgiDown(0.7);
printf("Data version: %s
\n", version);
}
/* Print lift information from trackDb, if any */
trackDbPrintOrigAssembly(tdb, database);
printUpdateTime(database, tdb, NULL);
}
if (tdb->html != NULL && tdb->html[0] != 0)
{
char *browserVersion;
if (btIE == cgiClientBrowser(&browserVersion, NULL, NULL) && *browserVersion < '8')
htmlHorizontalLine();
else // Move line down, since Description (in ->html) is proceded by too much space
printf("
");
printf("
\n");
jsonPrintGlobals(TRUE);
webEnd();
}
}
char *excludeVars[] = { "submit", "Submit", "g", NULL, "ajax", NULL,};
int main(int argc, char *argv[])
/* Process command line. */
{
cgiSpoof(&argc, argv);
htmlSetBackground(hBackgroundImage());
setUdcCacheDir();
cartEmptyShell(doMiddle, hUserCookie(), excludeVars, NULL);
return 0;
}