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/snpMap.c src/hg/cgilib/snpMap.c new file mode 100644 index 0000000..f6d2a59 --- /dev/null +++ src/hg/cgilib/snpMap.c @@ -0,0 +1,189 @@ +/* snpMap.c was originally generated by the autoSql program, which also + * generated snpMap.h and snpMap.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 "snpMap.h" + + +void snpMapStaticLoad(char **row, struct snpMap *ret) +/* Load a row from snpMap table into ret. The contents of ret will + * be replaced at the next call to this function. */ +{ + +ret->chrom = row[0]; +ret->chromStart = sqlUnsigned(row[1]); +ret->chromEnd = sqlUnsigned(row[2]); +ret->name = row[3]; +ret->source = row[4]; +ret->type = row[5]; +} + +struct snpMap *snpMapLoad(char **row) +/* Load a snpMap from row fetched with select * from snpMap + * from database. Dispose of this with snpMapFree(). */ +{ +struct snpMap *ret; + +AllocVar(ret); +ret->chrom = cloneString(row[0]); +ret->chromStart = sqlUnsigned(row[1]); +ret->chromEnd = sqlUnsigned(row[2]); +ret->name = cloneString(row[3]); +ret->source = cloneString(row[4]); +ret->type = cloneString(row[5]); +return ret; +} + +struct snpMap *snpMapLoadAll(char *fileName) +/* Load all snpMap from a whitespace-separated file. + * Dispose of this with snpMapFreeList(). */ +{ +struct snpMap *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[6]; + +while (lineFileRow(lf, row)) + { + el = snpMapLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct snpMap *snpMapLoadAllByChar(char *fileName, char chopper) +/* Load all snpMap from a chopper separated file. + * Dispose of this with snpMapFreeList(). */ +{ +struct snpMap *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[6]; + +while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) + { + el = snpMapLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct snpMap *snpMapLoadByQuery(struct sqlConnection *conn, char *query) +/* Load all snpMap 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 snpMapFreeList(). */ +{ +struct snpMap *list = NULL, *el; +struct sqlResult *sr; +char **row; + +sr = sqlGetResult(conn, query); +while ((row = sqlNextRow(sr)) != NULL) + { + el = snpMapLoad(row); + slAddHead(&list, el); + } +slReverse(&list); +sqlFreeResult(&sr); +return list; +} + +void snpMapSaveToDb(struct sqlConnection *conn, struct snpMap *el, char *tableName, int updateSize) +/* Save snpMap 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',%u,%u,'%s','%s','%s')", + tableName, el->chrom, el->chromStart, el->chromEnd, el->name, el->source, el->type); +sqlUpdate(conn, update->string); +freeDyString(&update); +} + + +struct snpMap *snpMapCommaIn(char **pS, struct snpMap *ret) +/* Create a snpMap out of a comma separated string. + * This will fill in ret if non-null, otherwise will + * return a new snpMap */ +{ +char *s = *pS; + +if (ret == NULL) + AllocVar(ret); +ret->chrom = sqlStringComma(&s); +ret->chromStart = sqlUnsignedComma(&s); +ret->chromEnd = sqlUnsignedComma(&s); +ret->name = sqlStringComma(&s); +ret->source = sqlStringComma(&s); +ret->type = sqlStringComma(&s); +*pS = s; +return ret; +} + +void snpMapFree(struct snpMap **pEl) +/* Free a single dynamically allocated snpMap such as created + * with snpMapLoad(). */ +{ +struct snpMap *el; + +if ((el = *pEl) == NULL) return; +freeMem(el->chrom); +freeMem(el->name); +freeMem(el->source); +freeMem(el->type); +freez(pEl); +} + +void snpMapFreeList(struct snpMap **pList) +/* Free a list of dynamically allocated snpMap's */ +{ +struct snpMap *el, *next; + +for (el = *pList; el != NULL; el = next) + { + next = el->next; + snpMapFree(&el); + } +*pList = NULL; +} + +void snpMapOutput(struct snpMap *el, FILE *f, char sep, char lastSep) +/* Print out snpMap. 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->name); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->source); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->type); +if (sep == ',') fputc('"',f); +fputc(lastSep,f); +} + +/* -------------------------------- End autoSql Generated Code -------------------------------- */ +