/* snp.c was originally generated by the autoSql program, which also 
 * generated snp.h and snp.sql.  This module links the database and
 * the RAM representation of objects. */

/* Copyright (C) 2014 The Regents of the University of California 
 * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */

#include "common.h"
#include "linefile.h"
#include "dystring.h"
#include "jksql.h"
#include "snp.h"


void snpStaticLoad(char **row, struct snp *ret)
/* Load a row from snp 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->observed = row[6];
ret->molType = row[7];
ret->class = row[8];
ret->valid = row[9];
ret->avHet = atof(row[10]);
ret->avHetSE = atof(row[11]);
ret->func = row[12];
ret->locType = row[13];
ret->source = row[14];
ret->exception = row[15];
}

struct snp *snpLoad(char **row)
/* Load a snp from row fetched with select * from snp
 * from database.  Dispose of this with snpFree(). */
{
struct snp *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->observed = cloneString(row[6]);
ret->molType = cloneString(row[7]);
ret->class = cloneString(row[8]);
ret->valid = cloneString(row[9]);
ret->avHet = atof(row[10]);
ret->avHetSE = atof(row[11]);
ret->func = cloneString(row[12]);
ret->locType = cloneString(row[13]);
ret->source = cloneString(row[14]);
ret->exception = cloneString(row[15]);
return ret;
}

struct snp *snpLoadAll(char *fileName) 
/* Load all snp from a whitespace-separated file.
 * Dispose of this with snpFreeList(). */
{
struct snp *list = NULL, *el;
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *row[16];

while (lineFileRow(lf, row))
    {
    el = snpLoad(row);
    slAddHead(&list, el);
    }
lineFileClose(&lf);
slReverse(&list);
return list;
}

struct snp *snpLoadAllByChar(char *fileName, char chopper) 
/* Load all snp from a chopper separated file.
 * Dispose of this with snpFreeList(). */
{
struct snp *list = NULL, *el;
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *row[16];

while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
    {
    el = snpLoad(row);
    slAddHead(&list, el);
    }
lineFileClose(&lf);
slReverse(&list);
return list;
}

struct snp *snpLoadByQuery(struct sqlConnection *conn, char *query)
/* Load all snp from table that satisfy the query given.  
 * Where query is of the form 'select * from example where something=something'
 * or 'select example.* from example, anotherTable where example.something = 
 * anotherTable.something'.
 * Dispose of this with snpFreeList(). */
{
struct snp *list = NULL, *el;
struct sqlResult *sr;
char **row;

sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
    {
    el = snpLoad(row);
    slAddHead(&list, el);
    }
slReverse(&list);
sqlFreeResult(&sr);
return list;
}

void snpSaveToDb(struct sqlConnection *conn, struct snp *el, char *tableName, int updateSize)
/* Save snp as a row to the table specified by tableName. 
 * As blob fields may be arbitrary size updateSize specifies the approx size
 * of a string that would contain the entire query. Arrays of native types are
 * converted to comma separated strings and loaded as such, User defined types are
 * inserted as NULL. Strings are automatically escaped to allow insertion into the database. */
{
struct dyString *update = dyStringNew(updateSize);
sqlDyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s','%s','%s','%s','%s',%g,%g,'%s','%s','%s','%s')", 
	tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->observed,  el->molType,  el->class,  el->valid,  el->avHet,  el->avHetSE,  el->func,  el->locType,  el->source,  el->exception);
sqlUpdate(conn, update->string);
dyStringFree(&update);
}


struct snp *snpCommaIn(char **pS, struct snp *ret)
/* Create a snp out of a comma separated string. 
 * This will fill in ret if non-null, otherwise will
 * return a new snp */
{
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->observed = sqlStringComma(&s);
ret->molType = sqlStringComma(&s);
ret->class = sqlStringComma(&s);
ret->valid = sqlStringComma(&s);
ret->avHet = sqlFloatComma(&s);
ret->avHetSE = sqlFloatComma(&s);
ret->func = sqlStringComma(&s);
ret->locType = sqlStringComma(&s);
ret->source = sqlStringComma(&s);
ret->exception = sqlStringComma(&s);
*pS = s;
return ret;
}

void snpFree(struct snp **pEl)
/* Free a single dynamically allocated snp such as created
 * with snpLoad(). */
{
struct snp *el;

if ((el = *pEl) == NULL) return;
freeMem(el->chrom);
freeMem(el->name);
freeMem(el->observed);
freeMem(el->molType);
freeMem(el->class);
freeMem(el->valid);
freeMem(el->func);
freeMem(el->locType);
freeMem(el->source);
freeMem(el->exception);
freez(pEl);
}

void snpFreeList(struct snp **pList)
/* Free a list of dynamically allocated snp's */
{
struct snp *el, *next;

for (el = *pList; el != NULL; el = next)
    {
    next = el->next;
    snpFree(&el);
    }
*pList = NULL;
}

void snpOutput(struct snp *el, FILE *f, char sep, char lastSep) 
/* Print out snp.  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->observed);
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->valid);
if (sep == ',') fputc('"',f);
fputc(sep,f);
fprintf(f, "%g", el->avHet);
fputc(sep,f);
fprintf(f, "%g", el->avHetSE);
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->locType);
if (sep == ',') fputc('"',f);
fputc(sep,f);
if (sep == ',') fputc('"',f);
fprintf(f, "%s", el->source);
if (sep == ',') fputc('"',f);
fputc(sep,f);
if (sep == ',') fputc('"',f);
fprintf(f, "%s", el->exception);
if (sep == ',') fputc('"',f);
fputc(lastSep,f);
}

/* -------------------------------- End autoSql Generated Code -------------------------------- */