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/gvUi.c src/hg/lib/gvUi.c
deleted file mode 100644
index a4f8682..0000000
--- src/hg/lib/gvUi.c
+++ /dev/null
@@ -1,353 +0,0 @@
-/* gvUi.c - char arrays for Genome Variation UI features */
-
-/* Copyright (C) 2014 The Regents of the University of California 
- * See README in this or parent directory for licensing information. */
-#include "gvUi.h"
-#include "common.h"
-#include "cart.h"
-#include "cheapcgi.h"
-
-
-/***************Filters**************/
-
-/* some stuff for mutation type choices */
-/* labels for checkboxes */
-char *gvTypeLabel[] = {
-    "substitution",
-    "insertion",
-    "duplication",
-    "deletion",
-    "complex",
-};
-
-/* names for checkboxes */
-char *gvTypeString[] = {
-    "gvPos.filter.sub",
-    "gvPos.filter.ins",
-    "gvPos.filter.dup",
-    "gvPos.filter.del",
-    "gvPos.filter.complex",
-};
-
-/* values in the db */
-char *gvTypeDbValue[] = {
-    "substitution",
-    "insertion",
-    "duplication",
-    "deletion",
-    "complex",
-};
-
-int gvTypeSize = ArraySize(gvTypeString);
-
-/* some stuff for the mutation location choices */
-/* labels for checkboxes */
-char *gvLocationLabel[] = {
-    "exon",
-    "intron",
-    "5' UTR",
-    "3' UTR",
-    "not within known transcription unit",
-};
-
-/* names for checkboxes */
-char *gvLocationString[] = {
-    "gvPos.filter.xon",
-    "gvPos.filter.intron",
-    "gvPos.filter.utr5",
-    "gvPos.filter.utr3",
-    "gvPos.filter.intergenic",
-};
-
-char *gvLocationDbValue[] = {
-    "exon",
-    "intron",
-    "5' UTR",
-    "3' UTR",
-    "not within known transcription unit",
-};
-
-int gvLocationSize = ArraySize(gvLocationLabel);
-
-char *gvSrcString[] = {
-    "gvPos.filter.src.SP",
-    "gvPos.filter.src.LSDB",
-};
-
-char *gvSrcDbValue[] = {
-    "UniProtKB",
-    "LSDB",
-};
-
-int gvSrcSize = ArraySize(gvSrcString);
-
-char *gvAccuracyLabel[] = {
-    "estimated coordinates",
-};
-
-char *gvAccuracyString[] = {
-    "gvPos.filter.estimate",
-};
-
-unsigned gvAccuracyDbValue[] = {
-    0,
-};
-
-int gvAccuracySize = ArraySize(gvAccuracyLabel);
-
-char *gvFilterDALabel[] = {
-    "phenotype-associated",
-    "not phenotype-associated",
-    "phenotype association unknown",
-};
-
-char *gvFilterDAString[] = {
-    "gvPos.filter.da.known",
-    "gvPos.filter.da.not",
-    "gvPos.filter.da.null",
-};
-
-char *gvFilterDADbValue[] = {
-    "phenotype-associated",
-    "not phenotype-associated",
-    "NULL",
-};
-
-int gvFilterDASize = ArraySize(gvFilterDAString);
-
-/***************Attribute display**************/
-
-/* list in display order of attribute type, key that is used in table */
-char *gvAttrTypeKey[] = {
-    "longName",
-    "commonName",
-    "alias",
-    "srcLink",
-    "links",
-    "mutType",
-    "rnaNtChange",
-    "protEffect",
-    "enzymeActivityFC",
-    "enzymeActivityQual",
-    "funChange",
-    "disease",
-    "phenoCommon",
-    "phenoOfficial",
-    "geneVarsDis",
-    "hap",
-    "ethnic",
-    "comment",
-    "userAnno",
-};
-
-/* list in display order of attribute type display names */
-char *gvAttrTypeDisplay[] = {
-    "Full name",
-    "Common name",
-    "Alias",
-    "External links",
-    "External links",
-    "Type of mutation",
-    "RNA nucleotide change",
-    "Effect on Protein",
-    "Enzyme activity, fold change relative to wild type",
-    "Qualitative effect on activity",
-    "Functional Change",
-    "Phenotype association",
-    "Phenotype common name",
-    "Phenotype official nomenclature",
-    "Variation and Disease information related to gene locus",
-    "Haplotype",
-    "Ethnicity/Nationality",
-    "Comments",
-    "User annotations",
-};
-
-/* category for each type above, match up by array index */
-char *gvAttrCategory[] = {
-    "Alias",
-    "Alias",
-    "Alias",
-    "Links",
-    "Links",
-    "RNA effect",
-    "RNA effect",
-    "Protein effect",
-    "Protein effect",
-    "Protein effect",
-    "Function",
-    "Patient/Subject phenotype",
-    "Patient/Subject phenotype",
-    "Patient/Subject phenotype",
-    "Data related to gene locus",
-    "Other Ancillary data",
-    "Other Ancillary data",
-    "Other Ancillary data",
-    "Other Ancillary data",
-};
-
-int gvAttrSize = ArraySize(gvAttrTypeKey);
-
-/***************Color options**************/
-
-char *gvColorLabels[] = {
-    "red",
-    "purple",
-    "green",
-    "orange",
-    "blue",
-    "brown",
-    "black",
-    "gray",
-};
-
-int gvColorLabelSize = ArraySize(gvColorLabels);
-
-char *gvColorTypeLabels[] = {
-    "substitution",
-    "insertion",
-    "duplication",
-    "deletion",
-    "complex",
-    "unknown",
-};
-
-char *gvColorTypeStrings[] = {
-    "gvColorTypeSub",
-    "gvColorTypeIns",
-    "gvColorTypeDup",
-    "gvColorTypeDel",
-    "gvColorTypeComplex",
-    "gvColorTypeUnk",
-};
-
-char *gvColorTypeDefault[] = {
-    "purple",
-    "green",
-    "orange",
-    "blue",
-    "brown",
-    "black",
-};
-
-char *gvColorTypeBaseChangeType[] = {
-    "substitution",
-    "insertion",
-    "duplication",
-    "deletion",
-    "complex",
-    "unknown",
-};
-
-/* all type arrays are same size */
-int gvColorTypeSize = ArraySize(gvColorTypeStrings);
-
-/* color by disease association */
-char *gvColorDALabels[] = {
-    "phenotype-associated",
-    "not phenotype-associated",
-    "phenotype association unknown",
-};
-
-char *gvColorDAStrings[] = {
-    "gvColorDAKnown",
-    "gvColorDANot",
-    "gvColorDARest",
-};
-
-char *gvColorDADefault[] = {
-    "red",
-    "green",
-    "gray",
-};
-
-char *gvColorDAAttrVal[] = {
-    "phenotype-associated",
-    "not phenotype-associated",
-    "NULL",
-};
-
-int gvColorDASize = ArraySize(gvColorDAStrings);
-
-void gvDisclaimer ()
-/* displays page with disclaimer forwarding query string that got us here */
-{
-struct cgiVar *cv, *cvList = cgiVarList();
-
-cartHtmlStart("PhenCode Disclaimer");
-printf("<TABLE WIDTH=\"%s\" BGCOLOR=\"#888888\" BORDER=\"0\" CELLSPACING=\"0\" CELLPADDING=\"1\"><TR><TD>", "100%");
-printf("<TABLE BGCOLOR=\"fffee8\" WIDTH=\"%s\"  BORDER=\"0\" CELLSPACING=\"0\" CELLPADDING=\"0\"><TR><TD>", "100%");
-printf("<TABLE BGCOLOR=\"D9E4F8\" BACKGROUND=\"../../images/hr.gif\" WIDTH=%s><TR><TD>", "100%");
-printf("<FONT SIZE=\"4\"><b>&nbsp;PhenCode Disclaimer </B></FONT> ");
-printf("</TD></TR></TABLE>");
-printf("<TABLE BGCOLOR=\"fffee8\" WIDTH=\"%s\" CELLPADDING=0><TR><TH HEIGHT=10></TH></TR>", "100%");
-printf("<TR><TD WIDTH=10>&nbsp;</TD><TD>");
-printf("<b>Usage</b>\n");
-printf("<p>\n");
-printf("PhenCode is intended for research purposes only.  Although the data\n");
-printf("are freely available to all, users should treat the reported mutations\n");
-printf("with extreme caution in clinical settings or for any diagnostic or\n");
-printf("population screening purpose.  This information requires expertise\n");
-printf("to interpret properly; clinical diagnosis and/or treatment\n");
-printf("recommendations should be made only by medical professionals.\n");
-printf("<p>\n");
-printf("Patients and doctors should not make treatment decisions based on the\n");
-printf("information in PhenCode.  In particular, <b>PhenCode should not be used\n");
-printf("to assess disease risk</b>.  Some of these variants are not associated\n");
-printf("with disease at all, and for many others the association is slight,\n");
-printf("depends on other factors, and/or may not be causative.  The mere fact\n");
-printf("that a variant is listed here does NOT mean that a particular patient\n");
-printf("will become ill.\n");
-printf("<p>");
-printf("<b>Errors</b>\n");
-printf("<p>\n");
-printf("The PhenCode track (including, but not limited to, \"Locus Variants\"\n");
-printf(") is a compilation of freely-available data\n");
-printf("obtained from other sources.  While reasonable effort is made to\n");
-printf("promote accuracy, nevertheless there may be errors in the original\n");
-printf("data and/or the compilation process.  <b>By using these data, you\n");
-printf("agree and acknowledge that the information is not guaranteed to be\n");
-printf("accurate.</b>  If you do find any errors, please report them to the\n");
-printf("addresses listed on the <a href=\"http://phencode.bx.psu.edu/phencode/contact.html\">Contact us</a> page.\n");
-printf("<p>");
-printf("<b>Disclaimer</b>\n");
-printf("<p>\n");
-printf("This resource and data are provided \"as is\", \"where is\" and without\n");
-printf("any express or implied warranties, including, but not limited to, any\n");
-printf("implied warranties of merchantability and/or fitness for a particular\n");
-printf("purpose.  In no event shall\n");
-printf("<a href=\"http://www.psu.edu/\">The Pennsylvania State University</a>,\n");
-printf("<a href=\"http://www.ucsc.edu/\">The University of California Santa Cruz</a>,\n");
-printf("or any data contributors,\n");
-printf("nor their respective agents, employees or representatives be liable\n");
-printf("for any direct, indirect, incidental, special, exemplary, or\n");
-printf("consequential damages (including, but not limited to, procurement of\n");
-printf("substitute goods or services; loss of use, data, or profits; business\n");
-printf("interruption; medical or legal expenses; or pain and suffering),\n");
-printf("however caused and on any theory of liability, whether in contract,\n");
-printf("strict liability, or tort (including negligence or otherwise) arising\n");
-printf("in any way or form out of the use of this resource or data, even if\n");
-printf("advised of the possibility of such damage.\n");
-printf("<p>\n");
-printf("Users assume all risk and responsibility for the accuracy,\n");
-printf("completeness, and usefulness, or lack thereof, of any information,\n");
-printf("apparatus, product, or process disclosed, and also all risk and\n");
-printf("responsibility that the use hereof would or would not infringe the\n");
-printf("rights of any other party.\n");
-printf("<p>\n");
-printf("<br>\n");
-printf("<FORM ACTION=\"%s\" METHOD=POST>\n", cgiScriptName());
-for (cv = cvList; cv != NULL; cv = cv->next)
-    {
-    cgiContinueHiddenVar(cv->name);
-    }
-cgiMakeButtonWithMsg("gvDisclaimer", "Agree", NULL);
-printf("&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;");
-cgiMakeButtonWithMsg("gvDisclaimer", "Disagree", NULL);
-printf("</FORM>\n");
-printf("</td></tr></table></td></tr></table></td></tr></table>");
-cartHtmlEnd();
-exit(0);
-}
-
-