// Create a new Merger using the provided kmerindex, query sequence, filter parameters and maximum inter-segment gap length.
// If selfCompare is true only the upper diagonal of the comparison matrix is examined.
func NewMerger(index *kmerindex.Index, query *seq.Seq, filterParams *Params, maxIGap int, selfCompare bool) *Merger {
tubeWidth := filterParams.TubeOffset + filterParams.MaxError
binWidth := tubeWidth - 1
leftPadding := diagonalPadding + binWidth
eoTerm := &Trapezoid{
Left: query.Len() + 1 + leftPadding,
Right: query.Len() + 1,
Bottom: -1,
Top: query.Len() + 1,
Next: nil,
}
return &Merger{
target: index.Seq,
filterParams: filterParams,
maxIGap: maxIGap,
query: query,
selfComparison: selfCompare,
bottomPadding: index.GetK() + 2,
leftPadding: leftPadding,
binWidth: binWidth,
eoTerm: eoTerm,
trapOrder: eoTerm,
}
}
// Return a new Filter using index as the target and filter parameters in params.
func New(index *kmerindex.Index, params *Params) (f *Filter) {
f = &Filter{
index: index,
target: index.Seq,
k: index.GetK(),
minMatch: params.MinMatch,
maxError: params.MaxError,
tubeOffset: params.TubeOffset,
}
return
}
// Create a new KmerRainbow defined by the rectangle r, kmerindex index and background color.
func NewKmerRainbow(r image.Rectangle, index *kmerindex.Index, background color.HSVA) *KmerRainbow { // should generalise the BG color
h := r.Dy()
kmers := make([]int, h)
kmask := util.Pow4(index.GetK())
kmaskf := float64(kmask)
f := func(index *kmerindex.Index, _, kmer int) {
kmers[int(float64(kmer)*float64(h)/kmaskf)]++
}
index.ForEachKmerOf(index.Seq, 0, index.Seq.Len(), f)
max := util.Max(kmers...)
return &KmerRainbow{
RGBA: image.NewRGBA(r),
Index: index,
Max: max,
BackGround: background,
}
}
// Create a new CGR defined by the kmerindex index and background color.
func NewCGR(index *kmerindex.Index, background color.HSVA) *CGR { // should generalise the BG color
max := 0
f := func(index *kmerindex.Index, _, kmer int) {
if freq := index.FingerAt(kmer); freq > max {
max = freq
}
}
index.ForEachKmerOf(index.Seq, 0, index.Seq.Len(), f)
k := uint(index.GetK())
return &CGR{
RGBA: image.NewRGBA(image.Rect(0, 0, 1<<k, 1<<k)),
Index: index,
Max: max,
BackGround: background,
}
}