struct linkedFeatures *lfFromRetroGene(struct ucscRetroInfo *pg)
/* Return a linked feature from a retroGene. */
{
struct linkedFeatures *lf;
struct simpleFeature *sf, *sfList = NULL;
int grayIx = grayInRange(pg->score, 0, 1000);
int *starts = pg->chromStarts, start;
int *sizes = pg->blockSizes;
int blockCount = pg->blockCount, i;
assert(starts != NULL && sizes != NULL && blockCount > 0);
AllocVar(lf);
lf->grayIx = grayIx;
lf->name = cloneString(pg->name);
lf->orientation = orientFromChar(pg->strand[0]);
for (i=0; i<blockCount; ++i)
{
AllocVar(sf);
start = starts[i] + pg->chromStart;
sf->start = start;
sf->end = start + sizes[i];
sf->grayIx = grayIx;
slAddHead(&sfList, sf);
}
slReverse(&sfList);
lf->components = sfList;
linkedFeaturesBoundsAndGrays(lf);
lf->tallStart = pg->thickStart;
lf->tallEnd = pg->thickEnd;
lf->extra = pg;
return lf;
}
static struct linkedFeatures *skeletonLf(struct cgapSage *tag)
/* Fill in everything except the name and score. */
{
struct linkedFeatures *lf;
struct simpleFeature *sf;
AllocVar(lf);
AllocVar(sf);
lf->start = sf->start = tag->chromStart;
lf->end = sf->end = tag->chromEnd;
lf->tallStart = tag->thickStart;
lf->tallEnd = tag->thickEnd;
lf->orientation = orientFromChar(tag->strand[0]);
lf->components = sf;
return lf;
}
static struct linkedFeatures *lfFromEncodePeak(struct slList *item, struct trackDb *tdb,
int scoreMin, int scoreMax)
/* Translate an {encode,narrow,broad,gapped}Peak item into a linkedFeatures. */
{
struct encodePeak *peak = (struct encodePeak *)item;
struct linkedFeatures *lf;
struct simpleFeature *sfList = NULL;
if (!peak)
return NULL;
AllocVar(lf);
lf->start = peak->chromStart;
lf->end = peak->chromEnd;
if (peak->peak > -1)
{
lf->tallStart = peak->chromStart + peak->peak;
lf->tallEnd = lf->tallStart + 1;
}
lf->filterColor = -1;
lf->orientation = orientFromChar(peak->strand[0]);
adjustBedScoreGrayLevel(tdb, (struct bed *)peak, scoreMin, scoreMax);
lf->grayIx = grayInRange((int)peak->score, scoreMin, scoreMax);
lf->name = cloneString(peak->name);
if (peak->blockCount > 0)
{
int i;
for (i = 0; i < peak->blockCount; i++)
{
struct simpleFeature *sf;
AllocVar(sf);
sf->start = lf->start + peak->blockStarts[i];
sf->end = lf->start + peak->blockStarts[i] + peak->blockSizes[i];
sf->grayIx = lf->grayIx;
slAddHead(&sfList, sf);
}
slReverse(&sfList);
}
else
{
AllocVar(sfList);
sfList->start = lf->start;
sfList->end = lf->end;
sfList->grayIx = lf->grayIx;
}
lf->components = sfList;
return lf;
}
struct linkedFeatures *lfFromBed6(struct codeBlast *bed, int scoreMin,
int scoreMax)
/* Return a linked feature from a (full) bed. */
{
struct linkedFeatures *lf;
struct simpleFeature *sf;
int grayIx = grayInRange(bed->score, scoreMin, scoreMax);
AllocVar(lf);
lf->grayIx = grayIx;
lf->name = cloneString(bed->name);
lf->orientation = orientFromChar(bed->strand[0]);
AllocVar(sf);
sf->start = bed->chromStart;
sf->end = bed->chromEnd;
sf->grayIx = grayIx;
lf->components = sf;
linkedFeaturesBoundsAndGrays(lf);
lf->tallStart = bed->chromStart;
lf->tallEnd = bed->chromEnd;
return lf;
}
struct linkedFeatures *lfFromSample(struct sample *sample)
/* Return a linked feature from a full sample (wiggle) track. */
{
struct linkedFeatures *lf;
struct simpleFeature *sf, *sfList = NULL;
int grayIx = grayInRange(sample->score, 0, 1000);
int start, i;
unsigned *X = sample->samplePosition;
int *Y = sample->sampleHeight;
unsigned sampleCount = sample->sampleCount;
assert(X != NULL && Y != NULL && sampleCount > 0);
AllocVar(lf);
lf->grayIx = grayIx;
lf->name = cloneString(sample->name);
lf->orientation = orientFromChar(sample->strand[0]);
for (i=0; i<sampleCount; ++i)
{
AllocVar(sf);
start = X[i] + sample->chromStart;
sf->start = start;
if( Y[i] < 0 ) /*hack for negative values not loading correctly*/
sf->end = start;
else if( Y[i] == 0 )
sf->end = start + 1;
else
sf->end = start + Y[i];
sf->grayIx = grayIx;
slAddHead(&sfList, sf);
}
slReverse(&sfList);
lf->components = sfList;
linkedFeaturesBoundsAndGrays(lf);
lf->start = sample->chromStart;
lf->end = sample->chromEnd;
return lf;
}
