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kmer_counts.go
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/* Copyright (C) 2019 Philipp Benner
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package gonetics
/* -------------------------------------------------------------------------- */
//import "fmt"
/* -------------------------------------------------------------------------- */
type KmerCounts struct {
// this is a sorted list of k-mers and might contain more entries than
// the counts map
Kmers KmerClassList
Counts map[KmerClassId]int
}
func (obj KmerCounts) Len() int {
return len(obj.Kmers)
}
func (obj KmerCounts) N() int {
return len(obj.Counts)
}
func (obj KmerCounts) At(i int) int {
if c, ok := obj.Counts[obj.Kmers[i].KmerClassId]; ok {
return c
} else {
return 0
}
}
func (obj KmerCounts) GetCount(kmer KmerClass) int {
if c, ok := obj.Counts[kmer.KmerClassId]; ok {
return c
} else {
return 0
}
}
func (obj KmerCounts) GetKmer(i int) KmerClass {
return obj.Kmers[i]
}
func (obj KmerCounts) Iterate() KmerCountsIterator {
return KmerCountsIterator{obj, 0}
}
func (obj *KmerCounts) SetKmers(kmers KmerClassList) {
counts := make(map[KmerClassId]int)
for _, kmer := range kmers {
if c, ok := obj.Counts[kmer.KmerClassId]; ok {
counts[kmer.KmerClassId] = c
}
}
obj.Kmers = kmers
obj.Counts = counts
}
/* -------------------------------------------------------------------------- */
type KmerCountsList struct {
Kmers KmerClassList
Counts []map[KmerClassId]int
}
func NewKmerCountsList(counts ...KmerCounts) KmerCountsList {
r := KmerCountsList{}
return r.Append(counts...)
}
func (obj KmerCountsList) Append(args ...KmerCounts) KmerCountsList {
if len(args) == 0 {
return obj
}
idLists := make([]KmerClassList, len(args))
counts := obj.Counts
for i, c := range args {
idLists[i] = c.Kmers
counts = append(counts, c.Counts)
}
ids := obj.Kmers.Union(idLists...)
return KmerCountsList{Kmers: ids, Counts: counts}
}
func (obj KmerCountsList) Len() int {
return len(obj.Counts)
}
func (obj KmerCountsList) At(i int) KmerCounts {
return KmerCounts{Kmers: obj.Kmers, Counts: obj.Counts[i]}
}
func (obj *KmerCountsList) Slice(i, j int) KmerCountsList {
return KmerCountsList{Kmers: obj.Kmers, Counts: obj.Counts[i:j]}
}
func (obj *KmerCountsList) SetKmers(kmers KmerClassList) {
for i := 0; i < obj.Len(); i++ {
counts := make(map[KmerClassId]int)
for _, kmer := range kmers {
if c, ok := obj.Counts[i][kmer.KmerClassId]; ok {
counts[kmer.KmerClassId] = c
}
}
obj.Counts[i] = counts
}
obj.Kmers = kmers
}
/* -------------------------------------------------------------------------- */
type KmerCountsIterator struct {
KmerCounts
i int
}
func (obj KmerCountsIterator) Ok() bool {
return obj.i < obj.Len()
}
func (obj KmerCountsIterator) GetKmer() KmerClass {
return obj.Kmers[obj.i]
}
func (obj KmerCountsIterator) GetCount() int {
return obj.At(obj.i)
}
func (obj KmerCountsIterator) GetIndex() int {
return obj.i
}
func (obj *KmerCountsIterator) Next() {
obj.i++
}