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/jaxQTL.c src/hg/cgilib/jaxQTL.c new file mode 100644 index 0000000..0261d65 --- /dev/null +++ src/hg/cgilib/jaxQTL.c @@ -0,0 +1,182 @@ +/* jaxQTL.c was originally generated by the autoSql program, which also + * generated jaxQTL.h and jaxQTL.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 "jaxQTL.h" + + +void jaxQTLStaticLoad(char **row, struct jaxQTL *ret) +/* Load a row from jaxQTL 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->score = sqlUnsigned(row[4]); +strcpy(ret->strand, row[5]); +ret->marker = row[6]; +ret->mgiID = row[7]; +ret->description = row[8]; +ret->cMscore = atof(row[9]); +} + +struct jaxQTL *jaxQTLLoad(char **row) +/* Load a jaxQTL from row fetched with select * from jaxQTL + * from database. Dispose of this with jaxQTLFree(). */ +{ +struct jaxQTL *ret; + +AllocVar(ret); +ret->chrom = cloneString(row[0]); +ret->chromStart = sqlUnsigned(row[1]); +ret->chromEnd = sqlUnsigned(row[2]); +ret->name = cloneString(row[3]); +ret->score = sqlUnsigned(row[4]); +strcpy(ret->strand, row[5]); +ret->marker = cloneString(row[6]); +ret->mgiID = cloneString(row[7]); +ret->description = cloneString(row[8]); +ret->cMscore = atof(row[9]); +return ret; +} + +struct jaxQTL *jaxQTLLoadAll(char *fileName) +/* Load all jaxQTL from a tab-separated file. + * Dispose of this with jaxQTLFreeList(). */ +{ +struct jaxQTL *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[10]; + +while (lineFileRow(lf, row)) + { + el = jaxQTLLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct jaxQTL *jaxQTLLoadWhere(struct sqlConnection *conn, char *table, char *where) +/* Load all jaxQTL from table that satisfy where clause. The + * where clause may be NULL in which case whole table is loaded + * Dispose of this with jaxQTLFreeList(). */ +{ +struct jaxQTL *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 = jaxQTLLoad(row); + slAddHead(&list, el); + } +slReverse(&list); +sqlFreeResult(&sr); +dyStringFree(&query); +return list; +} + +struct jaxQTL *jaxQTLCommaIn(char **pS, struct jaxQTL *ret) +/* Create a jaxQTL out of a comma separated string. + * This will fill in ret if non-null, otherwise will + * return a new jaxQTL */ +{ +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->score = sqlUnsignedComma(&s); +sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand)); +ret->marker = sqlStringComma(&s); +ret->mgiID = sqlStringComma(&s); +ret->description = sqlStringComma(&s); +ret->cMscore = sqlFloatComma(&s); +*pS = s; +return ret; +} + +void jaxQTLFree(struct jaxQTL **pEl) +/* Free a single dynamically allocated jaxQTL such as created + * with jaxQTLLoad(). */ +{ +struct jaxQTL *el; + +if ((el = *pEl) == NULL) return; +freeMem(el->chrom); +freeMem(el->name); +freeMem(el->marker); +freeMem(el->mgiID); +freeMem(el->description); +freez(pEl); +} + +void jaxQTLFreeList(struct jaxQTL **pList) +/* Free a list of dynamically allocated jaxQTL's */ +{ +struct jaxQTL *el, *next; + +for (el = *pList; el != NULL; el = next) + { + next = el->next; + jaxQTLFree(&el); + } +*pList = NULL; +} + +void jaxQTLOutput(struct jaxQTL *el, FILE *f, char sep, char lastSep) +/* Print out jaxQTL. 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, "%u", el->score); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->strand); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->marker); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->mgiID); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->description); +if (sep == ',') fputc('"',f); +fputc(sep,f); +fprintf(f, "%f", el->cMscore); +fputc(lastSep,f); +} +