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/pgSiftPred.c src/hg/lib/pgSiftPred.c deleted file mode 100644 index ab4f9ae..0000000 --- src/hg/lib/pgSiftPred.c +++ /dev/null @@ -1,261 +0,0 @@ -/* pgSiftPred.c was originally generated by the autoSql program, which also - * generated pgSiftPred.h and pgSiftPred.sql. This module links the database and - * the RAM representation of objects. */ - -/* Copyright (C) 2014 The Regents of the University of California - * See README in this or parent directory for licensing information. */ - -#include "common.h" -#include "linefile.h" -#include "dystring.h" -#include "jksql.h" -#include "hdb.h" -#include "pgSiftPred.h" - - -void pgSiftPredStaticLoadWithNull(char **row, struct pgSiftPred *ret) -/* Load a row from pgSiftPred table into ret. The contents of ret will - * be replaced at the next call to this function. */ -{ - -ret->chrom = row[0]; -if (row[1] != NULL) - { - ret->chromStart = needMem(sizeof(*(ret->chromStart))); - *(ret->chromStart) = sqlUnsigned(row[1]); - } -else - { - ret->chromStart = NULL; - } -if (row[2] != NULL) - { - ret->chromEnd = needMem(sizeof(*(ret->chromEnd))); - *(ret->chromEnd) = sqlUnsigned(row[2]); - } -else - { - ret->chromEnd = NULL; - } -ret->prediction = row[3]; -ret->geneId = row[4]; -ret->geneName = row[5]; -ret->geneDesc = row[6]; -ret->protFamDesc = row[7]; -ret->omimDisease = row[8]; -ret->aveAlleleFreq = row[9]; -ret->ceuAlleleFreq = row[10]; -} - -struct pgSiftPred *pgSiftPredLoadWithNull(char **row) -/* Load a pgSiftPred from row fetched with select * from pgSiftPred - * from database. Dispose of this with pgSiftPredFree(). */ -{ -struct pgSiftPred *ret; - -AllocVar(ret); -ret->chrom = cloneString(row[0]); -if (row[1] != NULL) - { - ret->chromStart = needMem(sizeof(*(ret->chromStart))); - *(ret->chromStart) = sqlUnsigned(row[1]); - } -else - { - ret->chromStart = NULL; - } -if (row[2] != NULL) - { - ret->chromEnd = needMem(sizeof(*(ret->chromEnd))); - *(ret->chromEnd) = sqlUnsigned(row[2]); - } -else - { - ret->chromEnd = NULL; - } -ret->prediction = cloneString(row[3]); -ret->geneId = cloneString(row[4]); -ret->geneName = cloneString(row[5]); -ret->geneDesc = cloneString(row[6]); -ret->protFamDesc = cloneString(row[7]); -ret->omimDisease = cloneString(row[8]); -ret->aveAlleleFreq = cloneString(row[9]); -ret->ceuAlleleFreq = cloneString(row[10]); -return ret; -} - -struct pgSiftPred *pgSiftPredLoadAll(char *fileName) -/* Load all pgSiftPred from a whitespace-separated file. - * Dispose of this with pgSiftPredFreeList(). */ -{ -struct pgSiftPred *list = NULL, *el; -struct lineFile *lf = lineFileOpen(fileName, TRUE); -char *row[11]; - -while (lineFileRow(lf, row)) - { - el = pgSiftPredLoadWithNull(row); - slAddHead(&list, el); - } -lineFileClose(&lf); -slReverse(&list); -return list; -} - -struct pgSiftPred *pgSiftPredLoadAllByChar(char *fileName, char chopper) -/* Load all pgSiftPred from a chopper separated file. - * Dispose of this with pgSiftPredFreeList(). */ -{ -struct pgSiftPred *list = NULL, *el; -struct lineFile *lf = lineFileOpen(fileName, TRUE); -char *row[11]; - -while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) - { - el = pgSiftPredLoadWithNull(row); - slAddHead(&list, el); - } -lineFileClose(&lf); -slReverse(&list); -return list; -} - -struct pgSiftPred *pgSiftPredCommaIn(char **pS, struct pgSiftPred *ret) -/* Create a pgSiftPred out of a comma separated string. - * This will fill in ret if non-null, otherwise will - * return a new pgSiftPred */ -{ -char *s = *pS; - -if (ret == NULL) - AllocVar(ret); -ret->chrom = sqlStringComma(&s); -ret->chromStart = needMem(sizeof(unsigned)); -*(ret->chromStart) = sqlUnsignedComma(&s); -ret->chromEnd = needMem(sizeof(unsigned)); -*(ret->chromEnd) = sqlUnsignedComma(&s); -ret->prediction = sqlStringComma(&s); -ret->geneId = sqlStringComma(&s); -ret->geneName = sqlStringComma(&s); -ret->geneDesc = sqlStringComma(&s); -ret->protFamDesc = sqlStringComma(&s); -ret->omimDisease = sqlStringComma(&s); -ret->aveAlleleFreq = sqlStringComma(&s); -ret->ceuAlleleFreq = sqlStringComma(&s); -*pS = s; -return ret; -} - -void pgSiftPredFree(struct pgSiftPred **pEl) -/* Free a single dynamically allocated pgSiftPred such as created - * with pgSiftPredLoad(). */ -{ -struct pgSiftPred *el; - -if ((el = *pEl) == NULL) return; -freeMem(el->chrom); -freeMem(el->prediction); -freeMem(el->geneId); -freeMem(el->geneName); -freeMem(el->geneDesc); -freeMem(el->protFamDesc); -freeMem(el->omimDisease); -freeMem(el->aveAlleleFreq); -freeMem(el->ceuAlleleFreq); -freez(pEl); -} - -void pgSiftPredFreeList(struct pgSiftPred **pList) -/* Free a list of dynamically allocated pgSiftPred's */ -{ -struct pgSiftPred *el, *next; - -for (el = *pList; el != NULL; el = next) - { - next = el->next; - pgSiftPredFree(&el); - } -*pList = NULL; -} - -void pgSiftPredOutput(struct pgSiftPred *el, FILE *f, char sep, char lastSep) -/* Print out pgSiftPred. Separate fields with sep. Follow last field with lastSep. */ -{ -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->chrom); -if (sep == ',') fputc('"',f); -fputc(sep,f); -fprintf(f, "%u", *(el->chromStart)); -fputc(sep,f); -fprintf(f, "%u", *(el->chromEnd)); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->prediction); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->geneId); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->geneName); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->geneDesc); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->protFamDesc); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->omimDisease); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->aveAlleleFreq); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->ceuAlleleFreq); -if (sep == ',') fputc('"',f); -fputc(lastSep,f); -} - -/* -------------------------------- End autoSql Generated Code -------------------------------- */ - -void printPgSiftPred (char *db, char *tableName, struct pgSnp *item) -/* print the predictions for an hgc item click for a pgSnp track */ -{ -struct pgSiftPred *el; -struct sqlResult *sr; -char **row; -char query[512]; -struct sqlConnection *conn = hAllocConn(db); - -sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and chromStart = %d and chromEnd = %d", - tableName, item->chrom, item->chromStart, item->chromEnd); -sr = sqlGetResult(conn, query); -while ((row = sqlNextRow(sr)) != NULL) - { - el = pgSiftPredLoadWithNull(row); - printf("<br><b>SIFT prediction</b>: %s\n", el->prediction); - printf("<ul>"); - if (el->geneId != NULL && differentString(el->geneId, "")) - printf("<li>Gene ID: %s</li>\n", el->geneId); - if (el->geneName != NULL && differentString(el->geneName, "")) - printf("<li>Gene name: %s</li>\n", el->geneName); - if (el->geneDesc != NULL && differentString(el->geneDesc, "")) - printf("<li>Gene description: %s</li>\n", el->geneDesc); - if (el->protFamDesc != NULL && differentString(el->protFamDesc, "")) - printf("<li>Protein family description: %s</li>\n", el->protFamDesc); - if (el->omimDisease != NULL && differentString(el->omimDisease, "")) - printf("<li>OMIM disease: %s</li>\n", el->omimDisease); - if (el->aveAlleleFreq != NULL && differentString(el->aveAlleleFreq, "")) - printf("<li>Average allele frequency: %s</li>\n", el->aveAlleleFreq); - if (el->ceuAlleleFreq != NULL && differentString(el->ceuAlleleFreq, "")) - printf("<li>CEU allele frequency: %s</li>\n", el->ceuAlleleFreq); - printf("</ul>\n"); - } -}