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("
", "100%"); -printf("
", "100%"); -printf("
", "100%"); -printf(" PhenCode Disclaimer "); -printf("
"); -printf("", "100%"); -printf("
 "); -printf("Usage\n"); -printf("

\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("

\n"); -printf("Patients and doctors should not make treatment decisions based on the\n"); -printf("information in PhenCode. In particular, PhenCode should not be used\n"); -printf("to assess disease risk. 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("

"); -printf("Errors\n"); -printf("

\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. By using these data, you\n"); -printf("agree and acknowledge that the information is not guaranteed to be\n"); -printf("accurate. If you do find any errors, please report them to the\n"); -printf("addresses listed on the Contact us page.\n"); -printf("

"); -printf("Disclaimer\n"); -printf("

\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("The Pennsylvania State University,\n"); -printf("The University of California Santa Cruz,\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("

\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("

\n"); -printf("
\n"); -printf("

\n", cgiScriptName()); -for (cv = cvList; cv != NULL; cv = cv->next) - { - cgiContinueHiddenVar(cv->name); - } -cgiMakeButtonWithMsg("gvDisclaimer", "Agree", NULL); -printf("        "); -cgiMakeButtonWithMsg("gvDisclaimer", "Disagree", NULL); -printf("
\n"); -printf("
"); -cartHtmlEnd(); -exit(0); -} - -