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/atomDb.c src/hg/cgilib/atomDb.c new file mode 100644 index 0000000..b390a0e --- /dev/null +++ src/hg/cgilib/atomDb.c @@ -0,0 +1,172 @@ +/* atomDb.c was originally generated by the autoSql program, which also + * generated atomDb.h and atomDb.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 "atomDb.h" + + +void atomStaticLoad(char **row, struct atom *ret) +/* Load a row from atom table into ret. The contents of ret will + * be replaced at the next call to this function. */ +{ + +ret->name = row[0]; +ret->instance = sqlUnsigned(row[1]); +ret->species = row[2]; +ret->chrom = row[3]; +ret->start = sqlUnsigned(row[4]); +ret->end = sqlUnsigned(row[5]); +safecpy(ret->strand, sizeof(ret->strand), row[6]); +ret->fivePrime = row[7]; +ret->threePrime = row[8]; +} + +struct atom *atomLoad(char **row) +/* Load a atom from row fetched with select * from atom + * from database. Dispose of this with atomFree(). */ +{ +struct atom *ret; + +AllocVar(ret); +ret->name = cloneString(row[0]); +ret->instance = sqlUnsigned(row[1]); +ret->species = cloneString(row[2]); +ret->chrom = cloneString(row[3]); +ret->start = sqlUnsigned(row[4]); +ret->end = sqlUnsigned(row[5]); +safecpy(ret->strand, sizeof(ret->strand), row[6]); +ret->fivePrime = cloneString(row[7]); +ret->threePrime = cloneString(row[8]); +return ret; +} + +struct atom *atomLoadAll(char *fileName) +/* Load all atom from a whitespace-separated file. + * Dispose of this with atomFreeList(). */ +{ +struct atom *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[9]; + +while (lineFileRow(lf, row)) + { + el = atomLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct atom *atomLoadAllByChar(char *fileName, char chopper) +/* Load all atom from a chopper separated file. + * Dispose of this with atomFreeList(). */ +{ +struct atom *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[9]; + +while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) + { + el = atomLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct atom *atomCommaIn(char **pS, struct atom *ret) +/* Create a atom out of a comma separated string. + * This will fill in ret if non-null, otherwise will + * return a new atom */ +{ +char *s = *pS; + +if (ret == NULL) + AllocVar(ret); +ret->name = sqlStringComma(&s); +ret->instance = sqlUnsignedComma(&s); +ret->species = sqlStringComma(&s); +ret->chrom = sqlStringComma(&s); +ret->start = sqlUnsignedComma(&s); +ret->end = sqlUnsignedComma(&s); +sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand)); +ret->fivePrime = sqlStringComma(&s); +ret->threePrime = sqlStringComma(&s); +*pS = s; +return ret; +} + +void atomFree(struct atom **pEl) +/* Free a single dynamically allocated atom such as created + * with atomLoad(). */ +{ +struct atom *el; + +if ((el = *pEl) == NULL) return; +freeMem(el->name); +freeMem(el->species); +freeMem(el->chrom); +freeMem(el->fivePrime); +freeMem(el->threePrime); +freez(pEl); +} + +void atomFreeList(struct atom **pList) +/* Free a list of dynamically allocated atom's */ +{ +struct atom *el, *next; + +for (el = *pList; el != NULL; el = next) + { + next = el->next; + atomFree(&el); + } +*pList = NULL; +} + +void atomOutput(struct atom *el, FILE *f, char sep, char lastSep) +/* Print out atom. Separate fields with sep. Follow last field with lastSep. */ +{ +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->name); +if (sep == ',') fputc('"',f); +fputc(sep,f); +fprintf(f, "%u", el->instance); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->species); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->chrom); +if (sep == ',') fputc('"',f); +fputc(sep,f); +fprintf(f, "%u", el->start); +fputc(sep,f); +fprintf(f, "%u", el->end); +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->fivePrime); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->threePrime); +if (sep == ',') fputc('"',f); +fputc(lastSep,f); +} + +/* -------------------------------- End autoSql Generated Code -------------------------------- */ +