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/cgilib/snpUi.c src/hg/cgilib/snpUi.c
new file mode 100644
index 0000000..534830d
--- /dev/null
+++ src/hg/cgilib/snpUi.c
@@ -0,0 +1,475 @@
+/* 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;
+