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/dbSnpRs.c src/hg/lib/dbSnpRs.c deleted file mode 100644 index e56a76d..0000000 --- src/hg/lib/dbSnpRs.c +++ /dev/null @@ -1,213 +0,0 @@ -/* dbSnpRs.c was originally generated by the autoSql program, which also - * generated dbSnpRs.h and dbSnpRs.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 "dbSnpRs.h" - - -void dbSnpRsStaticLoad(char **row, struct dbSnpRs *ret) -/* Load a row from dbSnpRs table into ret. The contents of ret will - * be replaced at the next call to this function. */ -{ - -ret->rsId = row[0]; -ret->avHet = atof(row[1]); -ret->avHetSE = atof(row[2]); -ret->valid = row[3]; -ret->allele1 = row[4]; -ret->allele2 = row[5]; -ret->assembly = row[6]; -ret->alternate = row[7]; -ret->func = row[8]; -} - -struct dbSnpRs *dbSnpRsLoad(char **row) -/* Load a dbSnpRs from row fetched with select * from dbSnpRs - * from database. Dispose of this with dbSnpRsFree(). */ -{ -struct dbSnpRs *ret; - -AllocVar(ret); -ret->rsId = cloneString(row[0]); -ret->avHet = atof(row[1]); -ret->avHetSE = atof(row[2]); -ret->valid = cloneString(row[3]); -ret->allele1 = cloneString(row[4]); -ret->allele2 = cloneString(row[5]); -ret->assembly = cloneString(row[6]); -ret->alternate = cloneString(row[7]); -ret->func = cloneString(row[8]); -return ret; -} - -struct dbSnpRs *dbSnpRsLoadAll(char *fileName) -/* Load all dbSnpRs from a whitespace-separated file. - * Dispose of this with dbSnpRsFreeList(). */ -{ -struct dbSnpRs *list = NULL, *el; -struct lineFile *lf = lineFileOpen(fileName, TRUE); -char *row[9]; - -while (lineFileRow(lf, row)) - { - el = dbSnpRsLoad(row); - slAddHead(&list, el); - } -lineFileClose(&lf); -slReverse(&list); -return list; -} - -struct dbSnpRs *dbSnpRsLoadAllByChar(char *fileName, char chopper) -/* Load all dbSnpRs from a chopper separated file. - * Dispose of this with dbSnpRsFreeList(). */ -{ -struct dbSnpRs *list = NULL, *el; -struct lineFile *lf = lineFileOpen(fileName, TRUE); -char *row[9]; - -while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) - { - el = dbSnpRsLoad(row); - slAddHead(&list, el); - } -lineFileClose(&lf); -slReverse(&list); -return list; -} - -struct dbSnpRs *dbSnpRsLoadByQuery(struct sqlConnection *conn, char *query) -/* Load all dbSnpRs from table that satisfy the query given. - * Where query is of the form 'select * from example where something=something' - * or 'select example.* from example, anotherTable where example.something = - * anotherTable.something'. - * Dispose of this with dbSnpRsFreeList(). */ -{ -struct dbSnpRs *list = NULL, *el; -struct sqlResult *sr; -char **row; - -sr = sqlGetResult(conn, query); -while ((row = sqlNextRow(sr)) != NULL) - { - el = dbSnpRsLoad(row); - slAddHead(&list, el); - } -slReverse(&list); -sqlFreeResult(&sr); -return list; -} - -void dbSnpRsSaveToDb(struct sqlConnection *conn, struct dbSnpRs *el, char *tableName, int updateSize) -/* Save dbSnpRs as a row to the table specified by tableName. - * As blob fields may be arbitrary size updateSize specifies the approx size - * of a string that would contain the entire query. Arrays of native types are - * converted to comma separated strings and loaded as such, User defined types are - * inserted as NULL. Strings are automatically escaped to allow insertion into the database. */ -{ -struct dyString *update = newDyString(updateSize); -sqlDyStringPrintf(update, "insert into %s values ( '%s',%f,%f,'%s','%s','%s','%s','%s','%s')", - tableName, el->rsId, el->avHet, el->avHetSE, el->valid, el->allele1, el->allele2, el->assembly, el->alternate, el->func); -sqlUpdate(conn, update->string); -freeDyString(&update); -} - - -struct dbSnpRs *dbSnpRsCommaIn(char **pS, struct dbSnpRs *ret) -/* Create a dbSnpRs out of a comma separated string. - * This will fill in ret if non-null, otherwise will - * return a new dbSnpRs */ -{ -char *s = *pS; - -if (ret == NULL) - AllocVar(ret); -ret->rsId = sqlStringComma(&s); -ret->avHet = sqlFloatComma(&s); -ret->avHetSE = sqlFloatComma(&s); -ret->valid = sqlStringComma(&s); -ret->allele1 = sqlStringComma(&s); -ret->allele2 = sqlStringComma(&s); -ret->assembly = sqlStringComma(&s); -ret->alternate = sqlStringComma(&s); -ret->func = sqlStringComma(&s); -*pS = s; -return ret; -} - -void dbSnpRsFree(struct dbSnpRs **pEl) -/* Free a single dynamically allocated dbSnpRs such as created - * with dbSnpRsLoad(). */ -{ -struct dbSnpRs *el; - -if ((el = *pEl) == NULL) return; -freeMem(el->rsId); -freeMem(el->valid); -freeMem(el->allele1); -freeMem(el->allele2); -freeMem(el->assembly); -freeMem(el->alternate); -freeMem(el->func); -freez(pEl); -} - -void dbSnpRsFreeList(struct dbSnpRs **pList) -/* Free a list of dynamically allocated dbSnpRs's */ -{ -struct dbSnpRs *el, *next; - -for (el = *pList; el != NULL; el = next) - { - next = el->next; - dbSnpRsFree(&el); - } -*pList = NULL; -} - -void dbSnpRsOutput(struct dbSnpRs *el, FILE *f, char sep, char lastSep) -/* Print out dbSnpRs. Separate fields with sep. Follow last field with lastSep. */ -{ -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->rsId); -if (sep == ',') fputc('"',f); -fputc(sep,f); -fprintf(f, "%f", el->avHet); -fputc(sep,f); -fprintf(f, "%f", el->avHetSE); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->valid); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->allele1); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->allele2); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->assembly); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->alternate); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->func); -if (sep == ',') fputc('"',f); -fputc(lastSep,f); -} - -/* -------------------------------- End autoSql Generated Code -------------------------------- */ -