e70152e44cc66cc599ff6b699eb8adc07f3e656a kent Sat May 24 21:09:34 2014 -0700 Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment. diff --git src/hg/lib/snpFasta.c src/hg/lib/snpFasta.c index 66a8746..c062140 100644 --- src/hg/lib/snpFasta.c +++ src/hg/lib/snpFasta.c @@ -1,181 +1,184 @@ /* snpFasta.c was originally generated by the autoSql program, which also * generated snpFasta.h and snpFasta.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 "snpFasta.h" void snpFastaStaticLoad(char **row, struct snpFasta *ret) /* Load a row from snpFasta table into ret. The contents of ret will * be replaced at the next call to this function. */ { ret->rsId = row[0]; ret->chrom = row[1]; ret->molType = row[2]; ret->class = row[3]; ret->observed = row[4]; ret->leftFlank = row[5]; ret->rightFlank = row[6]; } struct snpFasta *snpFastaLoad(char **row) /* Load a snpFasta from row fetched with select * from snpFasta * from database. Dispose of this with snpFastaFree(). */ { struct snpFasta *ret; AllocVar(ret); ret->rsId = cloneString(row[0]); ret->chrom = cloneString(row[1]); ret->molType = cloneString(row[2]); ret->class = cloneString(row[3]); ret->observed = cloneString(row[4]); ret->leftFlank = cloneString(row[5]); ret->rightFlank = cloneString(row[6]); return ret; } struct snpFasta *snpFastaLoadAll(char *fileName) /* Load all snpFasta from a whitespace-separated file. * Dispose of this with snpFastaFreeList(). */ { struct snpFasta *list = NULL, *el; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *row[7]; while (lineFileRow(lf, row)) { el = snpFastaLoad(row); slAddHead(&list, el); } lineFileClose(&lf); slReverse(&list); return list; } struct snpFasta *snpFastaLoadAllByChar(char *fileName, char chopper) /* Load all snpFasta from a chopper separated file. * Dispose of this with snpFastaFreeList(). */ { struct snpFasta *list = NULL, *el; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *row[7]; while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) { el = snpFastaLoad(row); slAddHead(&list, el); } lineFileClose(&lf); slReverse(&list); return list; } struct snpFasta *snpFastaCommaIn(char **pS, struct snpFasta *ret) /* Create a snpFasta out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new snpFasta */ { char *s = *pS; if (ret == NULL) AllocVar(ret); ret->rsId = sqlStringComma(&s); ret->chrom = sqlStringComma(&s); ret->molType = sqlStringComma(&s); ret->class = sqlStringComma(&s); ret->observed = sqlStringComma(&s); ret->leftFlank = sqlStringComma(&s); ret->rightFlank = sqlStringComma(&s); *pS = s; return ret; } void snpFastaFree(struct snpFasta **pEl) /* Free a single dynamically allocated snpFasta such as created * with snpFastaLoad(). */ { struct snpFasta *el; if ((el = *pEl) == NULL) return; freeMem(el->rsId); freeMem(el->chrom); freeMem(el->molType); freeMem(el->class); freeMem(el->observed); freeMem(el->leftFlank); freeMem(el->rightFlank); freez(pEl); } void snpFastaFreeList(struct snpFasta **pList) /* Free a list of dynamically allocated snpFasta's */ { struct snpFasta *el, *next; for (el = *pList; el != NULL; el = next) { next = el->next; snpFastaFree(&el); } *pList = NULL; } void snpFastaOutput(struct snpFasta *el, FILE *f, char sep, char lastSep) /* Print out snpFasta. Separate fields with sep. Follow last field with lastSep. */ { if (sep == ',') fputc('"',f); fprintf(f, "%s", el->rsId); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->chrom); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->molType); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->class); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->observed); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->leftFlank); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->rightFlank); if (sep == ',') fputc('"',f); fputc(lastSep,f); } /* -------------------------------- End autoSql Generated Code -------------------------------- */ void snpFastaTableCreate(struct sqlConnection *conn) /* create a snpFasta table */ { char *createString = "NOSQLINJ CREATE TABLE snpFasta (\n" " rsId varchar(255) not null, \n" " chrom varchar(255) not null, \n" " molType varchar(255) not null, \n" " class varchar(255) not null, \n" " observed longblob not null, \n" " leftFlank longblob not null, \n" " rightFlank longblob not null, \n" " INDEX rsId(rsId(12))\n" ");\n"; sqlRemakeTable(conn, "snpFasta", createString); }