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/recombRate.c src/hg/cgilib/recombRate.c new file mode 100644 index 0000000..1ee1237 --- /dev/null +++ src/hg/cgilib/recombRate.c @@ -0,0 +1,186 @@ +/* recombRate.c was originally generated by the autoSql program, which also + * generated recombRate.h and recombRate.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 "recombRate.h" + + +void recombRateStaticLoad(char **row, struct recombRate *ret) +/* Load a row from recombRate 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->decodeAvg = atof(row[4]); +ret->decodeFemale = atof(row[5]); +ret->decodeMale = atof(row[6]); +ret->marshfieldAvg = atof(row[7]); +ret->marshfieldFemale = atof(row[8]); +ret->marshfieldMale = atof(row[9]); +ret->genethonAvg = atof(row[10]); +ret->genethonFemale = atof(row[11]); +ret->genethonMale = atof(row[12]); +} + +struct recombRate *recombRateLoad(char **row) +/* Load a recombRate from row fetched with select * from recombRate + * from database. Dispose of this with recombRateFree(). */ +{ +struct recombRate *ret; + +AllocVar(ret); +ret->chrom = cloneString(row[0]); +ret->chromStart = sqlUnsigned(row[1]); +ret->chromEnd = sqlUnsigned(row[2]); +ret->name = cloneString(row[3]); +ret->decodeAvg = atof(row[4]); +ret->decodeFemale = atof(row[5]); +ret->decodeMale = atof(row[6]); +ret->marshfieldAvg = atof(row[7]); +ret->marshfieldFemale = atof(row[8]); +ret->marshfieldMale = atof(row[9]); +ret->genethonAvg = atof(row[10]); +ret->genethonFemale = atof(row[11]); +ret->genethonMale = atof(row[12]); +return ret; +} + +struct recombRate *recombRateLoadAll(char *fileName) +/* Load all recombRate from a tab-separated file. + * Dispose of this with recombRateFreeList(). */ +{ +struct recombRate *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[13]; + +while (lineFileRow(lf, row)) + { + el = recombRateLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct recombRate *recombRateLoadWhere(struct sqlConnection *conn, char *table, char *where) +/* Load all recombRate from table that satisfy where clause. The + * where clause may be NULL in which case whole table is loaded + * Dispose of this with recombRateFreeList(). */ +{ +struct recombRate *list = NULL, *el; +struct dyString *query = dyStringNew(256); +struct sqlResult *sr; +char **row; + +sqlDyStringPrintf(query, "select * from %s", table); +if (where != NULL) + dyStringPrintf(query, " where %s", where); +sr = sqlGetResult(conn, query->string); +while ((row = sqlNextRow(sr)) != NULL) + { + el = recombRateLoad(row); + slAddHead(&list, el); + } +slReverse(&list); +sqlFreeResult(&sr); +dyStringFree(&query); +return list; +} + +struct recombRate *recombRateCommaIn(char **pS, struct recombRate *ret) +/* Create a recombRate out of a comma separated string. + * This will fill in ret if non-null, otherwise will + * return a new recombRate */ +{ +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->decodeAvg = sqlFloatComma(&s); +ret->decodeFemale = sqlFloatComma(&s); +ret->decodeMale = sqlFloatComma(&s); +ret->marshfieldAvg = sqlFloatComma(&s); +ret->marshfieldFemale = sqlFloatComma(&s); +ret->marshfieldMale = sqlFloatComma(&s); +ret->genethonAvg = sqlFloatComma(&s); +ret->genethonFemale = sqlFloatComma(&s); +ret->genethonMale = sqlFloatComma(&s); +*pS = s; +return ret; +} + +void recombRateFree(struct recombRate **pEl) +/* Free a single dynamically allocated recombRate such as created + * with recombRateLoad(). */ +{ +struct recombRate *el; + +if ((el = *pEl) == NULL) return; +freeMem(el->chrom); +freeMem(el->name); +freez(pEl); +} + +void recombRateFreeList(struct recombRate **pList) +/* Free a list of dynamically allocated recombRate's */ +{ +struct recombRate *el, *next; + +for (el = *pList; el != NULL; el = next) + { + next = el->next; + recombRateFree(&el); + } +*pList = NULL; +} + +void recombRateOutput(struct recombRate *el, FILE *f, char sep, char lastSep) +/* Print out recombRate. 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); +fprintf(f, "%f", el->decodeAvg); +fputc(sep,f); +fprintf(f, "%f", el->decodeFemale); +fputc(sep,f); +fprintf(f, "%f", el->decodeMale); +fputc(sep,f); +fprintf(f, "%f", el->marshfieldAvg); +fputc(sep,f); +fprintf(f, "%f", el->marshfieldFemale); +fputc(sep,f); +fprintf(f, "%f", el->marshfieldMale); +fputc(sep,f); +fprintf(f, "%f", el->genethonAvg); +fputc(sep,f); +fprintf(f, "%f", el->genethonFemale); +fputc(sep,f); +fprintf(f, "%f", el->genethonMale); +fputc(lastSep,f); +} +