533112afe2a2005e80cdb1f82904ea65032d4302 braney Sat Oct 2 11:37:34 2021 -0700 split hg/lib into two separate libaries, one only used by the cgis diff --git src/hg/lib/snpUi.c src/hg/lib/snpUi.c deleted file mode 100644 index 534830d..0000000 --- src/hg/lib/snpUi.c +++ /dev/null @@ -1,475 +0,0 @@ -/* snpUi.c - char arrays for snp UI features */ - -/* Copyright (C) 2014 The Regents of the University of California - * See README in this or parent directory for licensing information. */ -#include "snpUi.h" -#include "common.h" - -/****** Some stuff for snp colors *******/ - -char *snpColorLabel[] = { - "red", - "green", - "blue", - "black", - "exclude", -}; - -int snpColorLabelSize = ArraySize(snpColorLabel); - -/****** Some stuff for snpMapSource related controls *******/ -/* dbSnp, Affy10K, Affy10Kv2, Affy50K_HindIII, Affy50K_XbaI */ - -char *snpMapSourceLabels[] = { - "Bac Overlaps", - "Random", - "Mixed", - "Other", - "Affymetrix Genotyping Array 10K", - "Affymetrix Genotyping Array 120K", -}; -char *snpMapSourceStrings[] = { - "snpMapSourceBacOverlap", - "snpMapSourceRandom", - "snpMapSourceMixed", - "snpMapSourceOther", - "snpMapSourceAffy10K", - "snpMapSourceAffy120K", -}; -char *snpMapSourceDataName[] = { - "BAC_OVERLAP", - "RANDOM", - "MIXED", - "OTHER", - "Affy10K", - "Affy120K", -}; -char *snpMapSourceDefault[] = { - "black", - "blue", - "red", - "red", - "green", - "green", -}; -char *snpMapSourceCart[] = { - "black", - "blue", - "red", - "red", - "green", - "green", -}; - -int snpMapSourceLabelsSize = ArraySize(snpMapSourceLabels); -int snpMapSourceStringsSize = ArraySize(snpMapSourceStrings); -int snpMapSourceDataNameSize = ArraySize(snpMapSourceDataName); -int snpMapSourceDefaultSize = ArraySize(snpMapSourceDefault); -int snpMapSourceCartSize = ArraySize(snpMapSourceCart); - -/****** Some stuff for snpMapType related controls *******/ -/* SingleNP, indel, segnemtal */ - -char *snpMapTypeLabel[] = { - "include", - "exclude", -}; -char *snpMapTypeLabels[] = { - "Single Nucleotide Polymorphisms", - "Insertions and Deletions", - "Segmental Duplications", -}; -char *snpMapTypeStrings[] = { - "snpMapTypeSingle", - "snpMapTypeIndels", - "snpMapTypeSegmental", -}; -char *snpMapTypeDataName[] = { - "SNP", - "INDEL", - "SEGMENTAL", -}; -char *snpMapTypeDefault[] = { - "include", - "include", - "include", -}; -char *snpMapTypeCart[] = { - "include", - "include", - "include", -}; - -int snpMapTypeLabelSize = ArraySize(snpMapTypeLabel); -int snpMapTypeLabelsSize = ArraySize(snpMapTypeLabels); -int snpMapTypeStringsSize = ArraySize(snpMapTypeStrings); -int snpMapTypeDataNameSize = ArraySize(snpMapTypeDataName); -int snpMapTypeDefaultSize = ArraySize(snpMapTypeDefault); -int snpMapTypeCartSize = ArraySize(snpMapTypeCart); - -/****** Some stuff for snpColorSource related controls *******/ -/* Source, Molecule Type, Class, Validation, Function */ - -char *snpColorSourceLabels[] = { - "Source", - "Molecule Type", - "Variant Class", - "Validation Status", - "Functional Class", - "Location Type", - "Black", -}; - -char *snpColorSourceStrings[] = { - "snpColorSourceSource", - "snpColorSourceMolType", - "snpColorSourceClass", - "snpColorSourceValid", - "snpColorSourceFunc", - "snpColorSourceLocType", - "snpColorSourceBlack", -}; -char *snpColorSourceDataName[] = { - "snpColorSource", -}; -char *snpColorSourceDefault[] = { - "snpColorSourceFunc", -}; -char *snpColorSourceCart[] = { - "snpColorSourceFunc", -}; - -int snpColorSourceLabelsSize = ArraySize(snpColorSourceLabels); -int snpColorSourceStringsSize = ArraySize(snpColorSourceStrings); -int snpColorSourceDataNameSize = ArraySize(snpColorSourceDataName); -int snpColorSourceDefaultSize = ArraySize(snpColorSourceDefault); -int snpColorSourceCartSize = ArraySize(snpColorSourceCart); - -/****** Some stuff for snpSource related controls *******/ -/* dbSnp, Affy10K, Affy10Kv2, Affy50K_HindIII, Affy50K_XbaI */ - -char *snpSourceLabels[] = { - "dbSnp", - "Affymetrix Genotyping Array 10K", - "Affymetrix Genotyping Array 10K v2", - "Affymetrix Genotyping Array 50K HindIII", - "Affymetrix Genotyping Array 50K XbaI", -}; -char *snpSourceStrings[] = { - "snpSourceDbSnp", - "snpSourceAffy10K", - "snpSourceAffy10Kv2", - "snpSourceAffy50KHindIII", - "snpSourceAffy50KXbaI", -}; -char *snpSourceDataName[] = { - "dbSnp", - "Affy10K", - "Affy10Kv2", - "Affy50K_HindIII", - "Affy50K_XbaI", -}; -char *snpSourceDefault[] = { - "black", - "blue", - "red", - "green", - "green", -}; -char *snpSourceCart[] = { - "black", - "blue", - "red", - "green", - "green", -}; - -int snpSourceLabelsSize = ArraySize(snpSourceLabels); -int snpSourceStringsSize = ArraySize(snpSourceStrings); -int snpSourceDataNameSize = ArraySize(snpSourceDataName); -int snpSourceDefaultSize = ArraySize(snpSourceDefault); -int snpSourceCartSize = ArraySize(snpSourceCart); - -/****** Some stuff for snpMolType related controls *******/ -/* unknown, genomic, cDNA, mito, chloro */ - -char *snpMolTypeLabels[] = { - "Unknown", - "Genomic", - "cDNA", - "Mitochondrial", - "Chloroplast", -}; -char *snpMolTypeStrings[] = { - "snpMolTypeUnknown", - "snpMolTypeGenomic", - "snpMolTypecDNA", - "snpMolTypeMito", - "snpMolTypeChloro", -}; -char *snpMolTypeDataName[] = { - "unknown", - "genomic", - "cDNA", - "mito", - "chloro", -}; -char *snpMolTypeDefault[] = { - "red", - "black", - "blue", - "green", - "exclude", -}; -char *snpMolTypeCart[] = { - "red", - "black", - "blue", - "green", - "exclude", -}; - -int snpMolTypeLabelsSize = ArraySize(snpMolTypeLabels); -int snpMolTypeStringsSize = ArraySize(snpMolTypeStrings); -int snpMolTypeDataNameSize = ArraySize(snpMolTypeDataName); -int snpMolTypeDefaultSize = ArraySize(snpMolTypeDefault); -int snpMolTypeCartSize = ArraySize(snpMolTypeCart); - -/****** Some stuff for snpClass related controls *******/ -/* unknown, snp, in-del, het, microsat, named, no-variation, mixed, - * mnp */ - -char *snpClassLabels[] = { - "Unknown", - "Single Nucleotide Polymorphism", - "Insertion / Deletion", - "Heterozygous", - "Microsatellite", - "Named", - "No Variation", - "Mixed", - "Multiple Nucleotide Polymorphism", -}; -char *snpClassStrings[] = { - "snpClassUnknown", - "snpClassSnp", - "snpClassInDel", - "snpClassHet", - "snpClassMicrosat", - "snpClassNamed", - "snpClassNoVariation", - "snpClassMixed", - "snpClassMnp", -}; -char *snpClassDataName[] = { - "unknown", - "snp", - "in-del", - "het", - "microsat", - "named", - "no-variation", - "mixed", - "mnp", -}; -char *snpClassDefault[] = { - "red", - "black", - "blue", - "red", - "green", - "green", - "red", - "black", - "blue", -}; -char *snpClassCart[] = { - "red", - "black", - "blue", - "red", - "green", - "green", - "red", - "black", - "blue", -}; - -int snpClassLabelsSize = ArraySize(snpClassLabels); -int snpClassStringsSize = ArraySize(snpClassStrings); -int snpClassDataNameSize = ArraySize(snpClassDataName); -int snpClassDefaultSize = ArraySize(snpClassDefault); -int snpClassCartSize = ArraySize(snpClassCart); - -/****** Some stuff for snpValid related controls *******/ -/* unknown, other-pop, by-frequency, by-cluster, by-2hit-2allele, - * by-hapmap, genotype */ - -char *snpValidLabels[] = { - "Unknown", - "Other Population", - "By Frequency", - "By Cluster", - "By 2 Hit / 2 Allele", - "By HapMap", - "By Genotype", -}; -char *snpValidStrings[] = { - "snpValidUnknown", - "snpValidOtherPop", - "snpValidFrequency", - "snpValidCluster", - "snpValid2H2A", - "snpValidHapMap", - "snpValidGenotype", -}; -char *snpValidDataName[] = { - "unknown", - "other-pop", - "by-frequency", - "by-cluster", - "by-2hit-2allele", - "by-hapmap", - "genotype", -}; -char *snpValidDefault[] = { - "red", - "black", - "black", - "black", - "black", - "blue", - "green", -}; -char *snpValidCart[] = { - "red", - "black", - "black", - "black", - "black", - "blue", - "green", -}; - -int snpValidLabelsSize = ArraySize(snpValidLabels); -int snpValidStringsSize = ArraySize(snpValidStrings); -int snpValidDataNameSize = ArraySize(snpValidDataName); -int snpValidDefaultSize = ArraySize(snpValidDefault); -int snpValidCartSize = ArraySize(snpValidCart); - -/****** Some stuff for snpFunc related controls *******/ -/* unknown, locus-region, coding, coding-synon, coding-nonsynon, - * mrna-utr, intron, splice-site, reference, exception */ - -char *snpFuncLabels[] = { - "Unknown", - "Locus Region", - "Coding", - "Coding - Synonymous", - "Coding - Non-Synonymous", - "mRNA/UTR", - "Intron", - "Splice site", - "Reference", - "Exception", -}; -char *snpFuncStrings[] = { - "snpFuncUnknown", - "snpFuncLocus", - "snpFuncCoding", - "snpFuncSynon", - "snpFuncNonSynon", - "snpFuncmRnaUtr", - "snpFuncIntron", - "snpFuncSplice", - "snpFuncReference", - "snpFuncException", -}; -char *snpFuncDataName[] = { - "unknown", - "locus-region", - "coding", - "coding-synon", - "coding-nonsynon", - "mrna-utr", - "intron", - "splice-site", - "reference", - "exception", -}; -char *snpFuncDefault[] = { - "black", - "black", - "blue", - "green", - "red", - "blue", - "blue", - "red", - "black", - "black", -}; -char *snpFuncCart[] = { - "black", - "black", - "blue", - "green", - "red", - "blue", - "blue", - "red", - "black", - "black", -}; - -int snpFuncLabelsSize = ArraySize(snpFuncLabels); -int snpFuncStringsSize = ArraySize(snpFuncStrings); -int snpFuncDataNameSize = ArraySize(snpFuncDataName); -int snpFuncDefaultSize = ArraySize(snpFuncDefault); -int snpFuncCartSize = ArraySize(snpFuncCart); - -/****** Some stuff for snpLocType related controls *******/ -/* unknown, range, exact, between */ - -char *snpLocTypeLabels[] = { - "Unknown", - "Range", - "Exact", - "Between", -}; -char *snpLocTypeStrings[] = { - "snpLocTypeUnknown", - "snpLocTypeRange", - "snpLocTypeExact", - "snpLocTypeBetween", -}; -char *snpLocTypeDataName[] = { - "unknown", - "range", - "exact", - "between", -}; -char *snpLocTypeDefault[] = { - "red", - "green", - "blue", - "black", -}; -char *snpLocTypeCart[] = { - "red", - "green", - "blue", - "black", -}; - -int snpLocTypeLabelsSize = ArraySize(snpLocTypeLabels); -int snpLocTypeStringsSize = ArraySize(snpLocTypeStrings); -int snpLocTypeDataNameSize = ArraySize(snpLocTypeDataName); -int snpLocTypeDefaultSize = ArraySize(snpLocTypeDefault); -int snpLocTypeCartSize = ArraySize(snpLocTypeCart); - -/****** Some stuff for snpLocType related controls *******/ -/* minimum Average Heterozygosity cutoff */ - -float snpAvHetCutoff = 0.0; -