struct zdobnovSynt *zdobnovSyntLoad(char **row)
/* Load a zdobnovSynt from row fetched with select * from zdobnovSynt
* from database. Dispose of this with zdobnovSyntFree(). */
{
struct zdobnovSynt *ret;
int sizeOne;
AllocVar(ret);
ret->blockCount = sqlSigned(row[9]);
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->thickStart = sqlUnsigned(row[6]);
ret->thickEnd = sqlUnsigned(row[7]);
ret->reserved = sqlUnsigned(row[8]);
sqlSignedDynamicArray(row[10], &ret->blockSizes, &sizeOne);
assert(sizeOne == ret->blockCount);
sqlSignedDynamicArray(row[11], &ret->chromStarts, &sizeOne);
assert(sizeOne == ret->blockCount);
sqlStringDynamicArray(row[12], &ret->geneNames, &sizeOne);
assert(sizeOne == ret->blockCount);
return ret;
}
struct splice *spliceLoad(char **row)
/* Load a splice from row fetched with select * from splice
* from database. Dispose of this with spliceFree(). */
{
struct splice *ret;
int sizeOne,i;
char *s;
AllocVar(ret);
ret->vCount = sqlSigned(row[7]);
ret->pathCount = sqlSigned(row[10]);
ret->tName = cloneString(row[0]);
ret->tStart = sqlSigned(row[1]);
ret->tEnd = sqlSigned(row[2]);
ret->name = cloneString(row[3]);
ret->type = sqlSigned(row[4]);
strcpy(ret->strand, row[5]);
ret->agxId = sqlSigned(row[6]);
sqlSignedDynamicArray(row[8], &ret->vPositions, &sizeOne);
assert(sizeOne == ret->vCount);
sqlUbyteDynamicArray(row[9], &ret->vTypes, &sizeOne);
assert(sizeOne == ret->vCount);
s = row[11];
for (i=0; i<ret->pathCount; ++i)
{
s = sqlEatChar(s, '{');
slSafeAddHead(&ret->paths, pathCommaIn(&s, NULL));
s = sqlEatChar(s, '}');
s = sqlEatChar(s, ',');
}
slReverse(&ret->paths);
return ret;
}
struct bigPsl *bigPslLoad(char **row)
/* Load a bigPsl from row fetched with select * from bigPsl
* from database. Dispose of this with bigPslFree(). */
{
struct bigPsl *ret;
AllocVar(ret);
ret->blockCount = sqlSigned(row[9]);
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->thickStart = sqlUnsigned(row[6]);
ret->thickEnd = sqlUnsigned(row[7]);
ret->reserved = sqlUnsigned(row[8]);
{
int sizeOne;
sqlSignedDynamicArray(row[10], &ret->blockSizes, &sizeOne);
assert(sizeOne == ret->blockCount);
}
{
int sizeOne;
sqlSignedDynamicArray(row[11], &ret->chromStarts, &sizeOne);
assert(sizeOne == ret->blockCount);
}
ret->oChromStart = sqlUnsigned(row[12]);
ret->oChromEnd = sqlUnsigned(row[13]);
safecpy(ret->oStrand, sizeof(ret->oStrand), row[14]);
ret->oChromSize = sqlUnsigned(row[15]);
{
int sizeOne;
sqlSignedDynamicArray(row[16], &ret->oChromStarts, &sizeOne);
assert(sizeOne == ret->blockCount);
}
ret->oSequence = cloneString(row[17]);
ret->oCDS = cloneString(row[18]);
ret->oBlock = sqlUnsigned(row[19]);
ret->match = sqlUnsigned(row[20]);
ret->misMatch = sqlUnsigned(row[21]);
ret->repMatch = sqlUnsigned(row[22]);
ret->nCount = sqlUnsigned(row[23]);
return ret;
}
struct pseudoGeneLink *pseudoGeneLinkLoad(char **row)
/* Load a pseudoGeneLink from row fetched with select * from pseudoGeneLink
* from database. Dispose of this with pseudoGeneLinkFree(). */
{
struct pseudoGeneLink *ret;
AllocVar(ret);
ret->blockCount = sqlSigned(row[9]);
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->thickStart = sqlUnsigned(row[6]);
ret->thickEnd = sqlUnsigned(row[7]);
ret->reserved = sqlUnsigned(row[8]);
{
int sizeOne;
sqlSignedDynamicArray(row[10], &ret->blockSizes, &sizeOne);
assert(sizeOne == ret->blockCount);
}
{
int sizeOne;
sqlSignedDynamicArray(row[11], &ret->chromStarts, &sizeOne);
assert(sizeOne == ret->blockCount);
}
ret->trfRatio = atof(row[12]);
ret->type = cloneString(row[13]);
ret->axtScore = sqlSigned(row[14]);
ret->gChrom = cloneString(row[15]);
ret->gStart = sqlSigned(row[16]);
ret->gEnd = sqlSigned(row[17]);
strcpy(ret->gStrand, row[18]);
ret->exonCount = sqlUnsigned(row[19]);
ret->geneOverlap = sqlUnsigned(row[20]);
ret->polyA = sqlUnsigned(row[21]);
ret->polyAstart = sqlSigned(row[22]);
ret->exonCover = sqlSigned(row[23]);
ret->intronCount = sqlUnsigned(row[24]);
ret->bestAliCount = sqlUnsigned(row[25]);
ret->matches = sqlUnsigned(row[26]);
ret->qSize = sqlUnsigned(row[27]);
ret->qEnd = sqlUnsigned(row[28]);
ret->tReps = sqlUnsigned(row[29]);
ret->overlapRhesus = sqlSigned(row[30]);
ret->overlapMouse = sqlSigned(row[31]);
ret->coverage = sqlUnsigned(row[32]);
ret->label = sqlSigned(row[33]);
ret->milliBad = sqlUnsigned(row[34]);
ret->oldScore = sqlUnsigned(row[35]);
ret->oldIntronCount = sqlSigned(row[36]);
ret->processedIntrons = sqlSigned(row[37]);
ret->conservedSpliceSites = sqlSigned(row[38]);
ret->maxOverlap = sqlSigned(row[39]);
ret->refSeq = cloneString(row[40]);
ret->rStart = sqlSigned(row[41]);
ret->rEnd = sqlSigned(row[42]);
ret->mgc = cloneString(row[43]);
ret->mStart = sqlSigned(row[44]);
ret->mEnd = sqlSigned(row[45]);
ret->kgName = cloneString(row[46]);
ret->kStart = sqlSigned(row[47]);
ret->kEnd = sqlSigned(row[48]);
ret->overName = cloneString(row[49]);
ret->overStart = sqlSigned(row[50]);
ret->overEnd = sqlSigned(row[51]);
strcpy(ret->overStrand, row[52]);
ret->overlapDog = sqlSigned(row[53]);
ret->posConf = atof(row[54]);
ret->polyAlen = sqlUnsigned(row[55]);
return ret;
}
