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/snpTmp.c src/hg/lib/snpTmp.c index 3050a2c..cf9e1fc 100644 --- src/hg/lib/snpTmp.c +++ src/hg/lib/snpTmp.c @@ -1,214 +1,217 @@ /* snpTmp.c was originally generated by the autoSql program, which also * generated snpTmp.h and snpTmp.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 "snpTmp.h" void snpTmpStaticLoad(char **row, struct snpTmp *ret) /* Load a row from snpTmp 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]; strcpy(ret->strand, row[4]); ret->refNCBI = row[5]; ret->locType = row[6]; ret->func = row[7]; ret->contigName = row[8]; } struct snpTmp *snpTmpLoad(char **row) /* Load a snpTmp from row fetched with select * from snpTmp * from database. Dispose of this with snpTmpFree(). */ { struct snpTmp *ret; AllocVar(ret); ret->chrom = cloneString(row[0]); ret->chromStart = sqlUnsigned(row[1]); ret->chromEnd = sqlUnsigned(row[2]); ret->name = cloneString(row[3]); strcpy(ret->strand, row[4]); ret->refNCBI = cloneString(row[5]); ret->locType = cloneString(row[6]); ret->func = cloneString(row[7]); ret->contigName = cloneString(row[8]); return ret; } struct snpTmp *snpTmpLoadAll(char *fileName) /* Load all snpTmp from a whitespace-separated file. * Dispose of this with snpTmpFreeList(). */ { struct snpTmp *list = NULL, *el; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *row[9]; while (lineFileRow(lf, row)) { el = snpTmpLoad(row); slAddHead(&list, el); } lineFileClose(&lf); slReverse(&list); return list; } struct snpTmp *snpTmpLoadAllByChar(char *fileName, char chopper) /* Load all snpTmp from a chopper separated file. * Dispose of this with snpTmpFreeList(). */ { struct snpTmp *list = NULL, *el; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *row[9]; while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) { el = snpTmpLoad(row); slAddHead(&list, el); } lineFileClose(&lf); slReverse(&list); return list; } struct snpTmp *snpTmpCommaIn(char **pS, struct snpTmp *ret) /* Create a snpTmp out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new snpTmp */ { char *s = *pS; if (ret == NULL) AllocVar(ret); ret->chrom = sqlStringComma(&s); ret->chromStart = sqlUnsignedComma(&s); ret->chromEnd = sqlUnsignedComma(&s); ret->name = sqlStringComma(&s); sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand)); ret->refNCBI = sqlStringComma(&s); ret->locType = sqlStringComma(&s); ret->func = sqlStringComma(&s); ret->contigName = sqlStringComma(&s); *pS = s; return ret; } void snpTmpFree(struct snpTmp **pEl) /* Free a single dynamically allocated snpTmp such as created * with snpTmpLoad(). */ { struct snpTmp *el; if ((el = *pEl) == NULL) return; freeMem(el->chrom); freeMem(el->name); freeMem(el->refNCBI); freeMem(el->locType); freeMem(el->func); freeMem(el->contigName); freez(pEl); } void snpTmpFreeList(struct snpTmp **pList) /* Free a list of dynamically allocated snpTmp's */ { struct snpTmp *el, *next; for (el = *pList; el != NULL; el = next) { next = el->next; snpTmpFree(&el); } *pList = NULL; } void snpTmpOutput(struct snpTmp *el, FILE *f, char sep, char lastSep) /* Print out snpTmp. 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); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->strand); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->refNCBI); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->locType); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->func); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->contigName); if (sep == ',') fputc('"',f); fputc(lastSep,f); } /* -------------------------------- End autoSql Generated Code -------------------------------- */ void snpTmpTableCreate(struct sqlConnection *conn, char *tableName) /* create a chrN_snpTmp table */ { char *createString = "CREATE TABLE %s (\n" " chrom varchar(255) not null,\n" " chromStart int unsigned not null,\n" " chromEnd int unsigned not null,\n" " name varchar(255) not null,\n" " strand char(1) not null,\n" " refNCBI longblob not null,\n" " locType enum('unknown', 'range', 'exact', 'between',\n" " 'rangeInsertion', 'rangeSubstitution', 'rangeDeletion') \n" " DEFAULT 'unknown' NOT NULL,\n" " func set( 'unknown', 'locus', 'coding', 'coding-synon', 'coding-nonsynon', \n" " 'untranslated', 'intron', 'splice-site', 'cds-reference') \n" " DEFAULT 'unknown' NOT NULL,\n" " # The functional category of the SNP\n" " contigName varchar(255) not null,\n" " INDEX name(name)\n" ")\n"; struct dyString *dy = newDyString(512); sqlDyStringPrintf(dy, createString, tableName); sqlRemakeTable(conn, tableName, dy->string); dyStringFree(&dy); } int snpTmpCmp(const void *va, const void *vb) { const struct snpTmp *a = *((struct snpTmp **)va); const struct snpTmp *b = *((struct snpTmp **)vb); int dif; dif = strcmp(a->chrom, b->chrom); if (dif == 0) dif = a->chromStart - b->chromStart; return dif; }