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

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



char *barChartBedCommaSepFieldNames = "chrom,chromStart,chromEnd,name,score,strand,name2,expCount,expScores,_dataOffset,_dataLen";

#ifdef NOT_SAFE
struct barChartBed *barChartBedLoadByQuery(struct sqlConnection *conn, char *query)
/* Load all barChartBed 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 barChartBedFreeList(). */
{
struct barChartBed *list = NULL, *el;
struct sqlResult *sr;
char **row;

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

void barChartBedSaveToDb(struct sqlConnection *conn, struct barChartBed *el, char *tableName, int updateSize)
/* Save barChartBed 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. This function automatically escapes quoted strings for mysql. */
{
struct dyString *update = dyStringNew(updateSize);
char  *expScoresArray;
expScoresArray = sqlFloatArrayToString(el->expScores, el->expCount);
sqlDyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s','%s',%u,'%s',%lld,%d)", 
	tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->name2,  el->expCount,  expScoresArray ,  el->_dataOffset,  el->_dataLen);
sqlUpdate(conn, update->string);
dyStringFree(&update);
freez(&expScoresArray);
}

#ifdef NOT_SAFE
struct barChartBed *barChartBedLoad(char **row)
/* Load a barChartBed from row fetched with select * from barChartBed
 * from database.  Dispose of this with barChartBedFree(). */
{
struct barChartBed *ret;

AllocVar(ret);
ret->expCount = sqlUnsigned(row[7]);
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]);
safecpy(ret->strand, sizeof(ret->strand), row[5]);
ret->name2 = cloneString(row[6]);
{
int sizeOne;
sqlFloatDynamicArray(row[8], &ret->expScores, &sizeOne);
assert(sizeOne == ret->expCount);
}
ret->_dataOffset = sqlLongLong(row[9]);
ret->_dataLen = sqlSigned(row[10]);
return ret;
}

struct barChartBed *barChartBedLoadAll(char *fileName) 
/* Load all barChartBed from a whitespace-separated file.
 * Dispose of this with barChartBedFreeList(). */
{
struct barChartBed *list = NULL, *el;
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *row[11];

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

struct barChartBed *barChartBedLoadAllByChar(char *fileName, char chopper) 
/* Load all barChartBed from a chopper separated file.
 * Dispose of this with barChartBedFreeList(). */
{
struct barChartBed *list = NULL, *el;
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *row[11];

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

#endif

struct barChartBed *barChartBedCommaIn(char **pS, struct barChartBed *ret)
/* Create a barChartBed out of a comma separated string. 
 * This will fill in ret if non-null, otherwise will
 * return a new barChartBed */
{
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->name2 = sqlStringComma(&s);
ret->expCount = sqlUnsignedComma(&s);
{
int i;
s = sqlEatChar(s, '{');
AllocArray(ret->expScores, ret->expCount);
for (i=0; i<ret->expCount; ++i)
    {
    ret->expScores[i] = sqlFloatComma(&s);
    }
s = sqlEatChar(s, '}');
s = sqlEatChar(s, ',');
}
ret->_dataOffset = sqlLongLongComma(&s);
ret->_dataLen = sqlSignedComma(&s);
*pS = s;
return ret;
}

void barChartBedFree(struct barChartBed **pEl)
/* Free a single dynamically allocated barChartBed such as created
 * with barChartBedLoad(). */
{
struct barChartBed *el;

if ((el = *pEl) == NULL) return;
freeMem(el->chrom);
freeMem(el->name);
freeMem(el->name2);
freeMem(el->expScores);
freez(pEl);
}

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

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

void barChartBedOutput(struct barChartBed *el, FILE *f, char sep, char lastSep) 
/* Print out barChartBed.  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->name2);
if (sep == ',') fputc('"',f);
fputc(sep,f);
fprintf(f, "%u", el->expCount);
fputc(sep,f);
{
int i;
if (sep == ',') fputc('{',f);
for (i=0; i<el->expCount; ++i)
    {
    fprintf(f, "%g", el->expScores[i]);
    fputc(',', f);
    }
if (sep == ',') fputc('}',f);
}
fputc(sep,f);
fprintf(f, "%lld", el->_dataOffset);
fputc(sep,f);
fprintf(f, "%d", el->_dataLen);
fputc(lastSep,f);
}

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

#include "basicBed.h"

void barChartBedCreateTable(struct sqlConnection *conn, char *table)
/* Create barChart format table of given name. */
{
char query[1024];

sqlSafef(query, sizeof(query),
"CREATE TABLE %s (\n"
"   chrom varchar(255) not null,        # Reference sequence chromosome or scaffold\n"
"   chromStart int unsigned not null,   # Start position in chromosome\n"
"   chromEnd int unsigned not null,     # End position in chromosome\n"
"   name varchar(255) not null,         # Identifier\n"
"   score int unsigned not null,        # Score from 0-1000\n"
"   strand char(1) not null,            # + or - for strand\n"
"   name2 varchar(255) not null,        # Alternative name for item\n"
"   expCount int unsigned not null,     # Number of experiment values\n"
"   expScores longblob not null,        # Comma separated list of experiment scores\n"
"   _dataOffset bigint not null,        # Offset of sample data in data matrix file, for boxplot on details page\n"
"   _dataLen int not null,              # Length of sample data row in data matrix file\n"
"   INDEX(name),\n"
"   INDEX(chrom(20), chromStart)\n"
")\n",
    table);
sqlRemakeTable(conn, table, query);
}

static char *barChartAutoSqlString =
"table barChartBed"
"\"BED6+5 with additional fields for category count and median values, and sample matrix fields\""
"    ("
"   string chrom;       \"Reference sequence chromosome or scaffold\""
"   uint   chromStart;  \"Start position in chromosome\""
"   uint   chromEnd;    \"End position in chromosome\""
"   string name;        \"Name or ID of item, ideally both human readable and unique\""
"   uint   score;       \"Score from 0-1000, typically derived from total of median value from all categories\""
"   char[1] strand;     \"+ or - for strand. Use . if not applicable\""
"   string name2;       \"Alternative name for item\""
"   uint expCount;      \"Number of categories\""
"   float[expCount] expScores; \"Comma separated list of category values\""
"   bigint _dataOffset; \"Offset of sample data in data matrix file, for boxplot on details page\""
"   int _dataLen;       \"Length of sample data row in data matrix file\""
"   )"
;

struct asObject *barChartAsObj()
/* Return asObject describing fields of barChart database table (includes bin) */
{
return asParseText(barChartAutoSqlString);
}


struct bed *barChartSimpleBedLoad(char **row)
/* Load a bed from row containing barChart bed fields. 
 * This reuses autoSql barChartBedLoad, but with a full-size bed.
 Dispose of this with bedFree() */
{
struct bed *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]);
safecpy(ret->strand, sizeof(ret->strand), row[5]);
// name2 is in row[6]
ret->expCount = sqlUnsigned(row[7]);
int sizeOne;
sqlFloatDynamicArray(row[8], &ret->expScores, &sizeOne);
if (sizeOne != ret->expCount)
    {
    warn("expScores mismatch");
    return NULL;
    }
return ret;
}

struct barChartBed *barChartBedLoadOptionalOffsets(char **row, boolean hasOffsets)
/* Load a barChartBed from row fetched with select * from barChartBed
 * from database or file.  Also supports schema lacking file offet and length for details.
.  Dispose of this with barChartBedFree(). */
{
struct barChartBed *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]);
safecpy(ret->strand, sizeof(ret->strand), row[5]);
ret->name2 = cloneString(row[6]);
ret->expCount = sqlUnsigned(row[7]);
int sizeOne;
sqlFloatDynamicArray(row[8], &ret->expScores, &sizeOne);
if (sizeOne != ret->expCount)
    {
    warn("expScores mismatch");
    return NULL;
    }
if (hasOffsets)
    {
    ret->_dataOffset = sqlLongLong(row[9]);
    ret->_dataLen = sqlSigned(row[10]);
    }
return ret;
}

float barChartTotalValue(struct barChartBed *bed)
/* Return total of all category values */
{
int i;
float sum = 0.0;
for (i=0; i<bed->expCount; i++)
    sum += bed->expScores[i];
return sum;
}

float barChartMaxValue(struct barChartBed *bed, int *categIdRet)
/* Return value and id of category with highest value for this item */
{
int i;
float maxScore = 0.0;
if (!categIdRet)
    return maxScore;
for (i=0; i<bed->expCount; i++)
    {
    float score = bed->expScores[i];
    if (score > maxScore)
        {
        maxScore = score;
        *categIdRet = i;
        }
    }
return maxScore;
}