static unsigned getLabelTypes(struct track *tg) /* get set of labels to use */ { unsigned labelSet = 0; // label setting are on parent track char prefix[128]; safef(prefix, sizeof(prefix), "%s.label", tg->tdb->track); struct hashEl *labels = cartFindPrefix(cart, prefix); if (labels == NULL) { // default to common name+accession and save this in cart so it makes sense in trackUi labelSet = useAcc; char setting[64]; safef(setting, sizeof(setting), "%s.label.gene", tg->tdb->track); cartSetBoolean(cart, setting, TRUE); } struct hashEl *label; for (label = labels; label != NULL; label = label->next) { if (endsWith(label->name, ".orgCommon") && differentString(label->val, "0")) labelSet |= useOrgCommon; else if (endsWith(label->name, ".orgAbbrv") && differentString(label->val, "0")) labelSet |= useOrgAbbrv; else if (endsWith(label->name, ".db") && differentString(label->val, "0")) labelSet |= useOrgDb; else if (endsWith(label->name, ".gene") && differentString(label->val, "0")) labelSet |= useGene; else if (endsWith(label->name, ".acc") && differentString(label->val, "0")) labelSet |= useAcc; } return labelSet; }
static void configAllVis(struct sqlConnection *conn, struct column *colList, boolean how) /* Respond to hide all button in configuration page. */ { char varName[64]; struct column *col; for (col = colList; col != NULL; col = col->next) { safef(varName, sizeof(varName), "%s%s.vis", colConfigPrefix, col->name); cartSetBoolean(cart, varName, how); } doConfigure(conn, colList); //, NULL); }
static struct dbTable *extraTableList(char *prefix) /* Get list of tables (other than the primary table) * where we are displaying fields. */ { struct hashEl *varList = NULL, *var; int prefixSize = strlen(prefix); struct dbTable *dtList = NULL, *dt; /* Build up list of tables to show by looking at * variables with right prefix in cart. */ varList = cartFindPrefix(cart, prefix); for (var = varList; var != NULL; var = var->next) { if (cartBoolean(cart, var->name)) { /* From variable name parse out database and table. */ char *dbTab = cloneString(var->name + prefixSize); char *db = dbTab; char *table = strchr(db, '.'); if (table == NULL) internalErr(); *table++ = 0; dt = dbTableNew(db, table); slAddHead(&dtList, dt); freez(&dbTab); } } if (varList == NULL && curTrack != NULL) { char *defaultLinkedTables = trackDbSetting(curTrack, "defaultLinkedTables"); if (defaultLinkedTables != NULL) { struct slName *t, *tables = slNameListFromString(defaultLinkedTables, ','); for (t = tables; t != NULL; t = t->next) { char varName[1024]; safef(varName, sizeof(varName), "%s%s.%s", prefix, database, t->name); cartSetBoolean(cart, varName, TRUE); dt = dbTableNew(database, t->name); slAddHead(&dtList, dt); } } } slSort(&dtList, dbTableCmp); return dtList; }
void jsMakeSetClearButton(struct cart *cart, char *form, char *buttonVar, char *buttonLabel, char *cartVarPrefix, struct slName *cartVarSuffixList, char *anchor, boolean currentPos, boolean isSet) /* Make a button for setting or clearing all of a list of boolean * cart variables (i.e. checkboxes). If this button was just pressed, * set or clear those cart variables. * Optional html anchor is appended to the form's action if given. * If currentPos, anchor is ignored and jsSetVerticalPosition is used so * that the new page gets the same vertical offset as the current page. */ { struct slName *suffix; char javascript[2048]; char *vertPosJs = ""; if (currentPos) { anchor = NULL; jsInit(); vertPosJs = jsSetVerticalPosition(form); } cgiMakeHiddenVar(buttonVar, ""); safef(javascript, sizeof javascript, "document.%s.action = '%s%s%s'; document.%s.%s.value='%s'; %s" "document.%s.submit();", form, cgiScriptName(), (isNotEmpty(anchor) ? "#" : ""), (isNotEmpty(anchor) ? anchor : ""), form, buttonVar, buttonLabel, vertPosJs, form); cgiMakeOnClickButton(javascript, buttonLabel); if (isNotEmpty(cgiOptionalString(buttonVar))) { char option[1024]; if (cartVarPrefix == NULL) cartVarPrefix = ""; for (suffix = cartVarSuffixList; suffix != NULL; suffix = suffix->next) { safef(option, sizeof(option), "%s%s", cartVarPrefix, suffix->name); cartSetBoolean(cart, option, isSet); } } }
void zooSpeciesHashInit() /* Function to init list of zoo species */ { char *name = NULL; char *val = NULL; if (zooSpeciesHash != NULL) return; zooSpeciesHash = hashNew(6); name = cloneString("Human"); val = cloneString("1"); hashAdd(zooSpeciesHash, name, val); cartSetBoolean( cart, "zooSpecies.Human", TRUE ); name = cloneString("Chimpanzee"); val = cloneString("2"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Baboon"); val = cloneString("3"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Orangutan"); val = cloneString("4"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Macaque"); val = cloneString("5"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Vervet"); val = cloneString("6"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Lemur"); val = cloneString("7"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Cat"); val = cloneString("8"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Dog"); val = cloneString("9"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Cow"); val = cloneString("10"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Pig"); val = cloneString("11"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Horse"); val = cloneString("12"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Rabbit"); val = cloneString("13"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Hedgehog"); val = cloneString("14"); hashAdd(zooSpeciesHash, name, val); name = cloneString("ajBat"); val = cloneString("15"); hashAdd(zooSpeciesHash, name, val); name = cloneString("cpBat"); val = cloneString("16"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Rat"); val = cloneString("17"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Mouse"); val = cloneString("18"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Platypus"); val = cloneString("19"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Opossum"); val = cloneString("20"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Dunnart"); val = cloneString("21"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Chicken"); val = cloneString("22"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Fugu"); val = cloneString("23"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Tetraodon"); val = cloneString("24"); hashAdd(zooSpeciesHash, name, val); name = cloneString("Zebrafish"); val = cloneString("25"); hashAdd(zooSpeciesHash, name, val); }
static void mafOrAxtClick2(struct sqlConnection *conn, struct sqlConnection *conn2, struct trackDb *tdb, char *axtOtherDb, char *fileName) /* Display details for MAF or AXT tracks. */ { hgBotDelay(); if (winEnd - winStart > 30000) { printf("Zoom so that window is 30,000 bases or less to see alignments and conservation statistics\n"); } else { struct mafAli *mafList = NULL, *maf, *subList = NULL; int aliIx = 0, realCount = 0; char dbChrom[64]; char option[128]; char *capTrack; struct consWiggle *consWig, *consWiggles; struct hash *speciesOffHash = NULL; char *speciesOrder = NULL; char *speciesTarget = trackDbSetting(tdb, SPECIES_TARGET_VAR); char buffer[1024]; int useTarg = FALSE; int useIrowChains = FALSE; safef(option, sizeof(option), "%s.%s", tdb->track, MAF_CHAIN_VAR); if (cartCgiUsualBoolean(cart, option, FALSE) && trackDbSetting(tdb, "irows") != NULL) useIrowChains = TRUE; safef(buffer, sizeof(buffer), "%s.vis",tdb->track); if (useIrowChains) { if (!cartVarExists(cart, buffer) && (speciesTarget != NULL)) useTarg = TRUE; else { char *val; val = cartUsualString(cart, buffer, "useCheck"); useTarg = sameString("useTarg",val); } } if (sameString(tdb->type, "bigMaf")) { char *fileName = trackDbSetting(tdb, "bigDataUrl"); struct bbiFile *bbi = bigBedFileOpen(fileName); mafList = bigMafLoadInRegion(bbi, seqName, winStart, winEnd); } else mafList = mafOrAxtLoadInRegion2(conn,conn2, tdb, seqName, winStart, winEnd, axtOtherDb, fileName); safef(dbChrom, sizeof(dbChrom), "%s.%s", hubConnectSkipHubPrefix(database), seqName); safef(option, sizeof(option), "%s.speciesOrder", tdb->track); speciesOrder = cartUsualString(cart, option, NULL); if (speciesOrder == NULL) speciesOrder = trackDbSetting(tdb, "speciesOrder"); for (maf = mafList; maf != NULL; maf = maf->next) { int mcCount = 0; struct mafComp *mc; struct mafAli *subset; struct mafComp *nextMc; /* remove empty components and configured off components * from MAF, and ignore * the entire MAF if all components are empty * (solely for gap annotation) */ if (!useTarg) { for (mc = maf->components->next; mc != NULL; mc = nextMc) { char buf[64]; char *organism; mafSrcDb(mc->src, buf, sizeof buf); organism = hOrganism(buf); if (!organism) organism = buf; nextMc = mc->next; safef(option, sizeof(option), "%s.%s", tdb->track, buf); if (!cartUsualBoolean(cart, option, TRUE)) { if (speciesOffHash == NULL) speciesOffHash = newHash(4); hashStoreName(speciesOffHash, organism); } if (!cartUsualBoolean(cart, option, TRUE)) slRemoveEl(&maf->components, mc); else mcCount++; } } if (mcCount == 0) continue; if (speciesOrder) { int speciesCt; char *species[2048]; struct mafComp **newOrder, *mcThis; int i; mcCount = 0; speciesCt = chopLine(cloneString(speciesOrder), species); newOrder = needMem((speciesCt + 1) * sizeof (struct mafComp *)); newOrder[mcCount++] = maf->components; for (i = 0; i < speciesCt; i++) { if ((mcThis = mafMayFindCompSpecies(maf, species[i], '.')) == NULL) continue; newOrder[mcCount++] = mcThis; } maf->components = NULL; for (i = 0; i < mcCount; i++) { newOrder[i]->next = 0; slAddHead(&maf->components, newOrder[i]); } slReverse(&maf->components); } subset = mafSubsetE(maf, dbChrom, winStart, winEnd, TRUE); if (subset != NULL) { /* Reformat MAF if needed so that sequence from current * database is the first component and on the * plus strand. */ mafMoveComponentToTop(subset, dbChrom); if (subset->components->strand == '-') mafFlipStrand(subset); subset->score = mafScoreMultiz(subset); slAddHead(&subList, subset); ++realCount; } } slReverse(&subList); mafAliFreeList(&mafList); if (subList != NULL) { char *showVarName = "hgc.showMultiBase"; char *showVarVal = cartUsualString(cart, showVarName, "all"); boolean onlyDiff = sameWord(showVarVal, "diff"); #ifdef ADDEXONCAPITAL char *codeVarName = "hgc.multiCapCoding"; char *codeVarVal = cartUsualString(cart, codeVarName, "coding"); boolean onlyCds = sameWord(codeVarVal, "coding"); #endif /* add links for conservation score statistics */ consWiggles = wigMafWiggles(database, tdb); int wigCount = slCount(consWiggles); if (wigCount == 1) { conservationStatsLink(tdb, "Conservation score statistics", consWiggles->table); } else if (wigCount > 1) { /* multiple wiggles. List all that have been turned on with * checkboxes */ /* Scan for cart variables -- do any exist, are any turned on ? */ boolean wigSet = FALSE; boolean wigOn = FALSE; for (consWig = consWiggles; consWig != NULL; consWig = consWig->next) { char *wigVarSuffix = NULL; (void)wigMafWiggleVar(tdb->track, consWig, &wigVarSuffix); if (cartVarExistsAnyLevel(cart, tdb, FALSE, wigVarSuffix)) { wigSet = TRUE; if (cartBooleanClosestToHome(cart, tdb, FALSE, wigVarSuffix)) wigOn = TRUE; } } /* If there are no cart vars, turn on the first (default) wig */ if (!wigSet) { char *prefix = tdb->track; // use when setting things to the cart if (tdbIsContainerChild(tdb)) prefix = tdbGetContainer(tdb)->track; cartSetBoolean(cart, wigMafWiggleVar(prefix, consWiggles, NULL), TRUE); wigOn = TRUE; } if (wigOn) { boolean first = TRUE; for (consWig = consWiggles; consWig != NULL; consWig = consWig->next) { if (first) { printf("Conservation score statistics:"); first = FALSE; } char *wigVarSuffix = NULL; (void)wigMafWiggleVar(tdb->track, consWig, &wigVarSuffix); if (cartUsualBooleanClosestToHome(cart, tdb, FALSE, wigVarSuffix,FALSE)) { printf(" "); subChar(consWig->uiLabel, '_', ' '); conservationStatsLink(tdb, consWig->uiLabel, consWig->table); } } } } puts("</P>\n"); /* no alignment to display when in visibilities where only wiggle is shown */ char *vis = cartOptionalString(cart, tdb->track); if (vis) { enum trackVisibility tv = hTvFromStringNoAbort(vis); if (tv == tvSquish || tv == tvDense) return; } #ifdef ADDEXONCAPITAL puts("<FORM ACTION=\"../cgi-bin/hgc\" NAME=\"gpForm\" METHOD=\"GET\">"); cartSaveSession(cart); cgiContinueHiddenVar("g"); cgiContinueHiddenVar("c"); cgiContinueHiddenVar("i"); printf("Capitalize "); cgiMakeDropListFull(codeVarName, codeAll, codeAll, ArraySize(codeAll), codeVarVal, autoSubmit); printf("exons based on "); capTrack = genePredDropDown(cart, trackHash, "gpForm", "hgc.multiCapTrack"); #endif printf("show "); cgiMakeDropListFull(showVarName, showAll, showAll, ArraySize(showAll), showVarVal, autoSubmit); printf("bases"); printf("<BR>\n"); printf("</FORM>\n"); #ifdef REVERSESTRAND /* notify if bases are complemented (hgTracks is on reverse strand) */ if (cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE)) puts("<EM>Alignment displayed on reverse strand</EM><BR>"); #endif puts("Place cursor over species for alignment detail. Click on 'B' to link to browser "); puts("for aligned species, click on 'D' to get DNA for aligned species.<BR>"); printf("<TT><PRE>"); /* notify if species removed from alignment */ if (speciesOffHash) { char *species; struct hashCookie hc = hashFirst(speciesOffHash); puts("<B>Components not displayed:</B> "); while ((species = hashNextName(&hc)) != NULL) printf("%s ", species); puts("<BR>"); } for (maf = subList; maf != NULL; maf = maf->next) { mafLowerCase(maf); #ifdef ADDEXONCAPITAL if (capTrack != NULL) capMafOnTrack(maf, capTrack, onlyCds); #endif printf("<B>Alignment block %d of %d in window, %d - %d, %d bps </B>\n", ++aliIx,realCount,maf->components->start + 1, maf->components->start + maf->components->size, maf->components->size); mafPrettyOut(stdout, maf, 70,onlyDiff, aliIx); } mafAliFreeList(&subList); } else { printf("No multiple alignment in browser window"); } printf("</PRE></TT>"); } }