BioKotlin/biokotlin.seq/ProteinSeq

ProteinSeq

interface ProteinSeq : Seq

Main data structure for working with Protein sequences

Inheritors

Functions

Link copied to clipboard
open fun back_translate(): NucSeq
Link copied to clipboard
abstract operator fun compareTo(other: Seq): Int
Link copied to clipboard
abstract operator fun contains(element: ProteinSeq): Boolean
Link copied to clipboard
abstract fun copyOfBytes(): ByteArray
Link copied to clipboard
abstract fun count(query: AminoAcid): Int
abstract fun count(query: ProteinSeq): Int
Link copied to clipboard
abstract fun count_overlap(query: ProteinSeq): Int
Link copied to clipboard
open fun find(query: ProteinSeq, start: Int = 0, end: Int = Int.MAX_VALUE): Int
Link copied to clipboard
abstract operator fun get(i: Int): AminoAcid

Returns on AminoAcid at the given position, if negative returns from the end of the sequence

abstract operator fun get(x: IntRange): ProteinSeq

Note Kotlin IntRange are inclusive end, while Python slices exclusive end Negative slices "-3..-1" start from the last base (i.e. would return the last three residues)

abstract operator fun get(i: Int, j: Int): ProteinSeq
Link copied to clipboard
abstract fun indexOf(query: ProteinSeq, start: Int = 0, end: Int = Int.MAX_VALUE): Int
Link copied to clipboard
abstract fun join(vararg seqs: ProteinSeq): ProteinSeq
Link copied to clipboard
abstract fun lastIndexOf(query: ProteinSeq, start: Int = 0, end: Int = Int.MAX_VALUE): Int
Link copied to clipboard
abstract operator fun plus(seq2: ProteinSeq): ProteinSeq
Link copied to clipboard
abstract fun repr(): String

Returns (truncated) representation of the sequence for debugging

Link copied to clipboard
open fun rfind(query: ProteinSeq, start: Int = 0, end: Int = Int.MAX_VALUE): Int
Link copied to clipboard
abstract fun seq(): String
Link copied to clipboard
abstract fun size(): Int

Returns the length of the sequence

Link copied to clipboard
abstract operator fun times(n: Int): ProteinSeq
Link copied to clipboard
abstract override fun toString(): String

Return the full sequence as string

Link copied to clipboard
abstract fun ungap(): Seq

TODO - needs to be implemented