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/ncRna.c src/hg/cgilib/ncRna.c new file mode 100644 index 0000000..7c9147a --- /dev/null +++ src/hg/cgilib/ncRna.c @@ -0,0 +1,179 @@ +/* ncRna.c was originally generated by the autoSql program, which also + * generated ncRna.h and ncRna.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 "ncRna.h" + + +void ncRnaStaticLoad(char **row, struct ncRna *ret) +/* Load a row from ncRna table into ret. The contents of ret will + * be replaced at the next call to this function. */ +{ + +ret->bin = sqlSigned(row[0]); +ret->chrom = row[1]; +ret->chromStart = sqlUnsigned(row[2]); +ret->chromEnd = sqlUnsigned(row[3]); +ret->name = row[4]; +ret->score = sqlSigned(row[5]); +strcpy(ret->strand, row[6]); +ret->thickStart = sqlUnsigned(row[7]); +ret->thickEnd = sqlUnsigned(row[8]); +ret->type = row[9]; +ret->extGeneId = row[10]; +} + +struct ncRna *ncRnaLoad(char **row) +/* Load a ncRna from row fetched with select * from ncRna + * from database. Dispose of this with ncRnaFree(). */ +{ +struct ncRna *ret; + +AllocVar(ret); +ret->bin = sqlSigned(row[0]); +ret->chrom = cloneString(row[1]); +ret->chromStart = sqlUnsigned(row[2]); +ret->chromEnd = sqlUnsigned(row[3]); +ret->name = cloneString(row[4]); +ret->score = sqlSigned(row[5]); +strcpy(ret->strand, row[6]); +ret->thickStart = sqlUnsigned(row[7]); +ret->thickEnd = sqlUnsigned(row[8]); +ret->type = cloneString(row[9]); +ret->extGeneId = cloneString(row[10]); +return ret; +} + +struct ncRna *ncRnaLoadAll(char *fileName) +/* Load all ncRna from a whitespace-separated file. + * Dispose of this with ncRnaFreeList(). */ +{ +struct ncRna *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[11]; + +while (lineFileRow(lf, row)) + { + el = ncRnaLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct ncRna *ncRnaLoadAllByChar(char *fileName, char chopper) +/* Load all ncRna from a chopper separated file. + * Dispose of this with ncRnaFreeList(). */ +{ +struct ncRna *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[11]; + +while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) + { + el = ncRnaLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct ncRna *ncRnaCommaIn(char **pS, struct ncRna *ret) +/* Create a ncRna out of a comma separated string. + * This will fill in ret if non-null, otherwise will + * return a new ncRna */ +{ +char *s = *pS; + +if (ret == NULL) + AllocVar(ret); +ret->bin = sqlSignedComma(&s); +ret->chrom = sqlStringComma(&s); +ret->chromStart = sqlUnsignedComma(&s); +ret->chromEnd = sqlUnsignedComma(&s); +ret->name = sqlStringComma(&s); +ret->score = sqlSignedComma(&s); +sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand)); +ret->thickStart = sqlUnsignedComma(&s); +ret->thickEnd = sqlUnsignedComma(&s); +ret->type = sqlStringComma(&s); +ret->extGeneId = sqlStringComma(&s); +*pS = s; +return ret; +} + +void ncRnaFree(struct ncRna **pEl) +/* Free a single dynamically allocated ncRna such as created + * with ncRnaLoad(). */ +{ +struct ncRna *el; + +if ((el = *pEl) == NULL) return; +freeMem(el->chrom); +freeMem(el->name); +freeMem(el->type); +freeMem(el->extGeneId); +freez(pEl); +} + +void ncRnaFreeList(struct ncRna **pList) +/* Free a list of dynamically allocated ncRna's */ +{ +struct ncRna *el, *next; + +for (el = *pList; el != NULL; el = next) + { + next = el->next; + ncRnaFree(&el); + } +*pList = NULL; +} + +void ncRnaOutput(struct ncRna *el, FILE *f, char sep, char lastSep) +/* Print out ncRna. Separate fields with sep. Follow last field with lastSep. */ +{ +fprintf(f, "%d", el->bin); +fputc(sep,f); +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, "%d", el->score); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->strand); +if (sep == ',') fputc('"',f); +fputc(sep,f); +fprintf(f, "%u", el->thickStart); +fputc(sep,f); +fprintf(f, "%u", el->thickEnd); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->type); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->extGeneId); +if (sep == ',') fputc('"',f); +fputc(lastSep,f); +} + +/* -------------------------------- End autoSql Generated Code -------------------------------- */ +