dbb7cbfd254794919a8e491cc3d3eb7c6009ba15 angie Tue Jan 25 14:58:05 2011 -0800 Track #1684 (SNPs 132 (dbSNP)): Added new coloring and filtering optionsfor new columns exceptions and bitfields. Fixed remaining hardcoded cart var names to use track name, keeping backwards compat with old sessions. Lots of refactoring -- got rid of snp125Extended business (mostly so I wouldn't have to make a snp132Extended); color is stored in snp->weight now, and extraName stuff overwrites name. Added new color-sorting in squish mode so the most interesting SNPs appear at the top. Also added new trackDb var defaultMaxWeight for the NonUnique subset (so its items aren't invisible by default). diff --git src/hg/lib/snp125Ui.c src/hg/lib/snp125Ui.c index 1c4ee8f..05c0a4e 100644 --- src/hg/lib/snp125Ui.c +++ src/hg/lib/snp125Ui.c @@ -1,430 +1,589 @@ /* snp125Ui.c - enums & char arrays for snp UI features and shared util code */ #include "snp125Ui.h" #include "common.h" static char const rcsid[] = "$Id: snp125Ui.c,v 1.33 2010/05/28 18:48:07 angie Exp $"; char *snp125OrthoTable(struct trackDb *tdb, int *retSpeciesCount) /* Look for a setting that specifies a table with orthologous alleles. * If retSpeciesCount is not null, set it to the number of other species * whose alleles are in the table. Do not free the returned string. */ { char *table = trackDbSetting(tdb, "chimpMacaqueOrthoTable"); int speciesCount = 2; if (table == NULL) { table = trackDbSetting(tdb, "chimpOrangMacOrthoTable"); speciesCount = 3; } if (retSpeciesCount != NULL) *retSpeciesCount = speciesCount; return table; } boolean snp125ExtendedNames = TRUE; /****** Some stuff for snp colors *******/ char *snp125ColorLabel[] = { "red", "green", "blue", "gray", "black", }; int snp125ColorArraySize = ArraySize(snp125ColorLabel); /****** color source controls *******/ /* This keeps track of which SNP feature is used for color definition. */ /* Available SNP features: Molecule Type, Class, Validation, Function */ char *snp125ColorSourceLabels[] = { "Location Type", "Class", "Validation", "Function", "Molecule Type", }; -char *snp125ColorSourceVarName = "snp125ColorSource"; -char *snp125ColorSourceDefault = "Function"; +char *snp125ColorSourceOldVar = "snp125ColorSource"; int snp125ColorSourceArraySize = ArraySize(snp125ColorSourceLabels); /* As of dbSNP 128, locType is ignored: */ char *snp128ColorSourceLabels[] = { "Class", "Validation", "Function", "Molecule Type", }; int snp128ColorSourceArraySize = ArraySize(snp128ColorSourceLabels); +/* As of dbSNP 132, we have some new choices: */ +char *snp132ColorSourceLabels[] = { + "Class", + "Validation", + "Function", + "Molecule Type", + "Unusual Conditions (UCSC)", + "Miscellaneous Attributes (dbSNP)", +}; + +int snp132ColorSourceArraySize = ArraySize(snp132ColorSourceLabels); + /****** MolType related controls *******/ /* Types: unknown, genomic, cDNA */ char *snp125MolTypeLabels[] = { "Unknown", "Genomic", "cDNA", }; -char *snp125MolTypeStrings[] = { +char *snp125MolTypeOldColorVars[] = { "snp125MolTypeUnknown", "snp125MolTypeGenomic", "snp125MolTypecDNA", }; char *snp125MolTypeDataName[] = { "unknown", "genomic", "cDNA", }; char *snp125MolTypeDefault[] = { "red", "black", "blue", }; -static char *snp125MolTypeOldVars[] = { +static char *snp125MolTypeOldIncludeVars[] = { "snp125MolTypeUnknownInclude", "snp125MolTypeGenomicInclude", "snp125MolTypecDNAInclude", }; int snp125MolTypeArraySize = ArraySize(snp125MolTypeLabels); /****** Class related controls *******/ /* Types: unknown, snp, in-del (locType exact), heterozygous, microsatellite, named, no variation, mixed, mnp, insertion (constructed from class = in-del, locType = between) deletion (constructed from class = in-del, locType = range) */ char *snp125ClassLabels[] = { "Unknown", "Single Nucleotide Polymorphism", "In/Del", "Heterozygous", "Microsatellite", "Named", "No Variation", "Mixed", "Mnp", "Insertion", "Deletion", }; -char *snp125ClassStrings[] = { +char *snp125ClassOldColorVars[] = { "snp125ClassUnknown", "snp125ClassSingle", "snp125ClassIn-del", "snp125ClassHet", "snp125ClassMicrosatellite", "snp125ClassNamed", "snp125ClassNoVar", "snp125ClassMixed", "snp125ClassMnp", "snp125ClassInsertion", "snp125ClassDeletion", }; char *snp125ClassDataName[] = { "unknown", "single", "in-del", "heterozygous", "microsatellite", "named", "no variation", "mixed", "mnp", "insertion", "deletion", }; char *snp125ClassDefault[] = { "red", // unknown "black", // single "black", // in-del "black", // het "blue", // microsatellite "blue", // named "black", // no variation "green", // mixed "green", // mnp "black", // insertion "red", // deletion }; -static char *snp125ClassOldVars[] = { +static char *snp125ClassOldIncludeVars[] = { "snp125ClassUnknownInclude", "snp125ClassSingleInclude", "snp125ClassIn-delInclude", "snp125ClassHetInclude", "snp125ClassMicrosatelliteInclude", "snp125ClassNamedInclude", "snp125ClassNoVarInclude", "snp125ClassMixedInclude", "snp125ClassMnpInclude", "snp125ClassInsertionInclude", "snp125ClassDeletionInclude", }; int snp125ClassArraySize = ArraySize(snp125ClassLabels); /****** Validation related controls *******/ /* Types: unknown, by-cluster, by-frequency, by-submitter, by-2hit-2allele, by-hapmap */ char *snp125ValidLabels[] = { "Unknown", "By Cluster", "By Frequency", "By Submitter", "By 2 Hit / 2 Allele", "By HapMap", "By 1000 Genomes Project", }; -char *snp125ValidStrings[] = { +char *snp125ValidOldColorVars[] = { "snp125ValidUnknown", "snp125ValidCluster", "snp125ValidFrequency", "snp125ValidSubmitter", "snp125Valid2H2A", "snp125ValidHapMap", "snp125Valid1000Genomes", }; char *snp125ValidDataName[] = { "unknown", "by-cluster", "by-frequency", "by-submitter", "by-2hit-2allele", "by-hapmap", "by-1000genomes", }; char *snp125ValidDefault[] = { "red", "black", "black", "black", "black", "green", "blue", }; -static char *snp125ValidOldVars[] = { +static char *snp125ValidOldIncludeVars[] = { "snp125ValidUnknownInclude", "snp125ValidClusterInclude", "snp125ValidFrequencyInclude", "snp125ValidSubmitterInclude", "snp125Valid2H2AInclude", "snp125ValidHapMapInclude", "snp125Valid1000GenomesInclude", }; int snp125ValidArraySize = ArraySize(snp125ValidLabels); /****** function related controls *******/ /* Values are a subset of snpNNN.func values: * unknown, locus, coding, coding-synon, coding-nonsynon, * untranslated, intron, splice-site, cds-reference */ char *snp125FuncLabels[] = { "Unknown", "Locus", "Coding - Synonymous", "Coding - Non-Synonymous", "Untranslated", "Intron", "Splice Site", "Reference (coding)", }; -char *snp125FuncStrings[] = { +char *snp125FuncOldColorVars[] = { "snp125FuncUnknown", "snp125FuncLocus", "snp125FuncSynon", "snp125FuncNonSynon", "snp125FuncUntranslated", "snp125FuncIntron", "snp125FuncSplice", "snp125FuncReference", }; char *snp125FuncDataName[] = { "unknown", "locus", "coding-synon", "coding-nonsynon", "untranslated", "intron", "splice-site", "cds-reference", }; char *snp125FuncDefault[] = { "black", // unknown "black", // locus "green", // coding-synon "red", // coding-nonsynon "blue", // untranslated "black", // intron "red", // splice-site "black", // cds-reference }; /* NCBI has added some new, more specific function types that map onto * pre-existing simpler function classes. This mapping is an array of * arrays, each of which has the simpler type (from snp125FuncDataName * above) followed by more specific subtypes, if any. All arrays are * NULL-terminated. */ static char *locusSyn[] = {"locus", "gene-segment", "near-gene-3", "near-gene-5", NULL}; static char *nonsynonSyn[] = {"coding-nonsynon", "nonsense", "missense", "frameshift", "cds-indel", "coding-synonymy-unknown", NULL}; static char *untranslatedSyn[] = {"untranslated", "untranslated-3", "untranslated-5", NULL}; static char *spliceSyn[] = {"splice-site", "splice-3", "splice-5", NULL}; static char *cdsRefSyn[] = {"cds-reference", "coding", NULL}; char **snp125FuncDataSynonyms[] = { locusSyn, nonsynonSyn, untranslatedSyn, spliceSyn, cdsRefSyn, NULL }; -static char *snp125FuncOldVars[] = { +static char *snp125FuncOldIncludeVars[] = { "snp125FuncUnknownInclude", "snp125FuncLocusInclude", "snp125FuncSynonInclude", "snp125FuncNonSynonInclude", "snp125FuncUntranslatedInclude", "snp125FuncIntronInclude", "snp125FuncSpliceInclude", "snp125FuncReferenceInclude", }; int snp125FuncArraySize = ArraySize(snp125FuncLabels); /****** LocType related controls *******/ /* Types: unknown, range, exact, between, rangeInsertion, rangeSubstitution, rangeDeletion */ char *snp125LocTypeLabels[] = { "Unknown", "Range", "Exact", "Between", "RangeInsertion", "RangeSubstitution", "RangeDeletion", }; -char *snp125LocTypeStrings[] = { +char *snp125LocTypeOldColorVars[] = { "snp125LocTypeUnknown", "snp125LocTypeRange", "snp125LocTypeExact", "snp125LocTypeBetween", "snp125LocTypeRangeInsertion", "snp125LocTypeRangeSubstitution", "snp125LocTypeDeletion", }; char *snp125LocTypeDataName[] = { "unknown", "range", "exact", "between", "rangeInsertion", "rangeSubstitution", "rangeDeletion", }; char *snp125LocTypeDefault[] = { "black", "red", "black", "blue", "green", "green", "green", }; -static char *snp125LocTypeOldVars[] = { +static char *snp125LocTypeOldIncludeVars[] = { "snp125LocTypeUnknownInclude", "snp125LocTypeRangeInclude", "snp125LocTypeExactInclude", "snp125LocTypeBetweenInclude", "snp125LocTypeRangeInsertionInclude", "snp125LocTypeRangeSubstitutionInclude", "snp125LocTypeRangeDeletionInclude", }; int snp125LocTypeArraySize = ArraySize(snp125LocTypeLabels); +/****** Exception related controls *******/ +char *snp132ExceptionLabels[] = { + "None", + "RefAlleleMismatch", + "RefAlleleRevComp", + "DuplicateObserved", + "MixedObserved", + "FlankMismatchGenomeLonger", + "FlankMismatchGenomeEqual", + "FlankMismatchGenomeShorter", + "NamedDeletionZeroSpan", + "NamedInsertionNonzeroSpan", + "SingleClassLongerSpan", + "SingleClassZeroSpan", + "SingleClassTriAllelic", + "SingleClassQuadAllelic", + "ObservedWrongFormat", + "ObservedTooLong", + "ObservedContainsIupac", + "ObservedMismatch", + "MultipleAlignments", + "NonIntegerChromCount", + "AlleleFreqSumNot1", +}; + +char *snp132ExceptionVarName[] = { + "NoExceptions", + "RefAlleleMismatch", + "RefAlleleRevComp", + "DuplicateObserved", + "MixedObserved", + "FlankMismatchGenomeLonger", + "FlankMismatchGenomeEqual", + "FlankMismatchGenomeShorter", + "NamedDeletionZeroSpan", + "NamedInsertionNonzeroSpan", + "SingleClassLongerSpan", + "SingleClassZeroSpan", + "SingleClassTriAllelic", + "SingleClassQuadAllelic", + "ObservedWrongFormat", + "ObservedTooLong", + "ObservedContainsIupac", + "ObservedMismatch", + "MultipleAlignments", + "NonIntegerChromCount", + "AlleleFreqSumNot1", +}; + +char *snp132ExceptionDefault[] = { + "black", // NoExceptions + "red", // RefAlleleMismatch + "red", // RefAlleleRevComp + "red", // DuplicateObserved + "red", // MixedObserved + "red", // FlankMismatchGenomeLonger + "red", // FlankMismatchGenomeEqual + "red", // FlankMismatchGenomeShorter + "red", // NamedDeletionZeroSpan + "red", // NamedInsertionNonzeroSpan + "red", // SingleClassLongerSpan + "red", // SingleClassZeroSpan + "gray", // SingleClassTriAllelic + "gray", // SingleClassQuadAllelic + "red", // ObservedWrongFormat + "gray", // ObservedTooLong + "gray", // ObservedContainsIupac + "red", // ObservedMismatch + "red", // MultipleAlignments + "gray", // NonIntegerChromCount + "gray", // AlleleFreqSumNot1 +}; + +int snp132ExceptionArraySize = ArraySize(snp132ExceptionLabels); + +/****** Miscellaneous attributes (dbSNP's bitfields) related controls *******/ + +char *snp132BitfieldLabels[] = { + "None", + "Clinically Associated", + "MAF >= 5% in Some Population", + "MAF >= 5% in All Populations", + "Appears in OMIM/OMIA", + "Has Microattribution/Third-Party Annotation", + "Submitted by Locus-Specific Database", + "Genotype Conflict", + "Ref SNP Cluster has Nonoverlapping Alleles", + "Some Assembly's Allele Does Not Match Observed", +}; + +char *snp132BitfieldVarName[] = { + "NoBitfields", + "ClinicallyAssoc", + "Maf5SomePop", + "Maf5AllPops", + "HasOmimOmia", + "MicroattrTpa", + "SubmittedByLsdb", + "GenotypeConflict", + "RsClusterNonoverlappingAlleles", + "DbSnpObservedMismatch", +}; + +char *snp132BitfieldDataName[] = { + "", + "clinically-assoc", + "maf-5-some-pop", + "maf-5-all-pops", + "has-omim-omia", + "microattr-tpa", + "submitted-by-lsdb", + "genotype-conflict", + "rs-cluster-nonoverlapping-alleles", + "observed-mismatch", +}; + +char *snp132BitfieldDefault[] = { + "black", // NoBitfields + "red", // ClinicallyAssoc + "blue", // Maf5SomePop + "green", // Maf5AllPops + "red", // HasOmimOmia + "red", // MicroattrTpa + "red", // SubmittedByLsdb + "gray", // GenotypeConflict + "gray", // RsClusterNonoverlappingAlleles + "gray", // DbSnpObservedMismatch +}; + +int snp132BitfieldArraySize = ArraySize(snp132BitfieldLabels); + + struct slName *snp125FilterFromCart(struct cart *cart, char *track, char *attribute, boolean *retFoundInCart) /* Look up snp125 filter settings in the cart, keeping backwards compatibility with old * cart variable names. */ { struct slName *values = NULL; boolean foundInCart = FALSE; char cartVar[256]; safef(cartVar, sizeof(cartVar), "%s.include_%s", track, attribute); if (cartListVarExists(cart, cartVar)) { foundInCart = TRUE; values = cartOptionalSlNameList(cart, cartVar); } else { char **oldVarNames = NULL, **oldDataName = NULL; int oldArraySize = 0; if (sameString(attribute, "molType")) { - oldVarNames = snp125MolTypeOldVars; + oldVarNames = snp125MolTypeOldIncludeVars; oldDataName = snp125MolTypeDataName; oldArraySize = snp125MolTypeArraySize; } else if (sameString(attribute, "class")) { - oldVarNames = snp125ClassOldVars; + oldVarNames = snp125ClassOldIncludeVars; oldDataName = snp125ClassDataName; oldArraySize = snp125ClassArraySize; } else if (sameString(attribute, "valid")) { - oldVarNames = snp125ValidOldVars; + oldVarNames = snp125ValidOldIncludeVars; oldDataName = snp125ValidDataName; oldArraySize = snp125ValidArraySize; } else if (sameString(attribute, "func")) { - oldVarNames = snp125FuncOldVars; + oldVarNames = snp125FuncOldIncludeVars; oldDataName = snp125FuncDataName; oldArraySize = snp125FuncArraySize; } else if (sameString(attribute, "locType")) { - oldVarNames = snp125LocTypeOldVars; + oldVarNames = snp125LocTypeOldIncludeVars; oldDataName = snp125LocTypeDataName; oldArraySize = snp125LocTypeArraySize; } if (oldVarNames != NULL) { int i; for (i=0; i < oldArraySize; i++) if (cartVarExists(cart, oldVarNames[i])) { foundInCart = TRUE; break; } if (foundInCart) { for (i=0; i < oldArraySize; i++) if (cartUsualBoolean(cart, oldVarNames[i], TRUE)) slNameAddHead(&values, oldDataName[i]); } } } if (retFoundInCart != NULL) *retFoundInCart = foundInCart; return values; } +char *snp125OldColorVarToNew(char *oldVar, char *attribute) +/* Abbreviate an old cart var name -- new name is based on track plus this. Don't free result. */ +{ +char *ptr = oldVar; +if (startsWith("snp125", oldVar)) + { + ptr += strlen("snp125"); + char upCaseAttribute[256]; + safecpy(upCaseAttribute, sizeof(upCaseAttribute), attribute); + upCaseAttribute[0] = toupper(upCaseAttribute[0]); + if (startsWith(upCaseAttribute, ptr)) + ptr += strlen(upCaseAttribute); + } +return ptr; +} +