Protein

Type Members

abstract class AASymbol extends Symbol
sealed abstract class AminoAcid extends AASymbol
case class Codon(aa: AminoAcid, codon: List[NTSymbol]) extends CodonSymbol with Product with Serializable

The Codon stores an (ambiguous) AminoAcid with the matching DNA sequence (also ambiguous, and including gaps).
The Codon stores an (ambiguous) AminoAcid with the matching DNA sequence (also ambiguous, and including gaps). Note that this is the most open implementation with the purpose of storing codons and their amino acids in matching alignments.
sealed abstract class CodonGap extends CodonSymbol
class CodonSequence extends bio.Sequence[Codon]

Store a list of Codon AminoAcids with their Codon sequences.
Store a list of Codon AminoAcids with their Codon sequences. The sequence is initialized from the DNA sequence, before translation. For example
val s = new CodonSequence("agctaacgt") s(2) should equal (R) s(2).getCodon should equal (List(C,G,T))
sealed abstract class CodonSymbol extends AnyRef
sealed abstract class Gap extends AASymbol
class GappedCodonSequence extends bio.Sequence[CodonSymbol]
class GappedSequence extends bio.Sequence[AASymbol]
abstract class HydrophobicAminoAcid extends AminoAcid
sealed abstract class IUPAC extends AminoAcid
class IUPACGappedSequence extends bio.Sequence[AASymbol]
class IUPACSequence extends bio.Sequence[AminoAcid]
abstract class NegativeAminoAcid extends AminoAcid
abstract class PositiveAminoAcid extends AminoAcid
class Sequence extends bio.Sequence[AminoAcid]
abstract class SpecialAminoAcid extends AminoAcid
abstract class UnchargedAminoAcid extends AminoAcid

Value Members

object * extends AminoAcid with Product with Serializable
object A extends HydrophobicAminoAcid with Product with Serializable
object AminoAcidConvert extends StringConverter[AminoAcid]
object B extends IUPAC with Product with Serializable
object C extends UnchargedAminoAcid with Product with Serializable
object CodonGap extends CodonGap with Product with Serializable
object D extends NegativeAminoAcid with Product with Serializable
object DNAtoCodon
object E extends NegativeAminoAcid with Product with Serializable
object F extends HydrophobicAminoAcid with Product with Serializable
object G extends UnchargedAminoAcid with Product with Serializable
object Gap extends Gap with Product with Serializable
object GappedConvert extends GappedConvert[AASymbol]
object GappedDNAtoCodon
object H extends PositiveAminoAcid with Product with Serializable
object I extends HydrophobicAminoAcid with Product with Serializable
object IUPACAminoAcidConvert extends StringConverter[AminoAcid]
object IUPACGappedAminoAcidConvert extends StringConverter[AASymbol]
object IUPACGappedConvert extends GappedConvert[AASymbol]
object K extends PositiveAminoAcid with Product with Serializable
object L extends HydrophobicAminoAcid with Product with Serializable
object M extends HydrophobicAminoAcid with Product with Serializable
object N extends UnchargedAminoAcid with Product with Serializable
object P extends UnchargedAminoAcid with Product with Serializable
object Q extends UnchargedAminoAcid with Product with Serializable
object R extends PositiveAminoAcid with Product with Serializable
object S extends UnchargedAminoAcid with Product with Serializable
object SymbolConvert extends StringConverter[AASymbol]
object T extends UnchargedAminoAcid with Product with Serializable
object U extends UnchargedAminoAcid with Product with Serializable
object V extends HydrophobicAminoAcid with Product with Serializable
object W extends HydrophobicAminoAcid with Product with Serializable
object X extends IUPAC with Product with Serializable
object Y extends HydrophobicAminoAcid with Product with Serializable
object Z extends IUPAC with Product with Serializable

package Protein

Type Members

abstract class AASymbol extends Symbol

sealed abstract class AminoAcid extends AASymbol

case class Codon(aa: AminoAcid, codon: List[NTSymbol]) extends CodonSymbol with Product with Serializable

sealed abstract class CodonGap extends CodonSymbol

class CodonSequence extends bio.Sequence[Codon]

sealed abstract class CodonSymbol extends AnyRef

sealed abstract class Gap extends AASymbol

class GappedCodonSequence extends bio.Sequence[CodonSymbol]

class GappedSequence extends bio.Sequence[AASymbol]

abstract class HydrophobicAminoAcid extends AminoAcid

sealed abstract class IUPAC extends AminoAcid

class IUPACGappedSequence extends bio.Sequence[AASymbol]

class IUPACSequence extends bio.Sequence[AminoAcid]

abstract class NegativeAminoAcid extends AminoAcid

abstract class PositiveAminoAcid extends AminoAcid

class Sequence extends bio.Sequence[AminoAcid]

abstract class SpecialAminoAcid extends AminoAcid

abstract class UnchargedAminoAcid extends AminoAcid

Value Members

object * extends AminoAcid with Product with Serializable

object A extends HydrophobicAminoAcid with Product with Serializable

object AminoAcidConvert extends StringConverter[AminoAcid]

object B extends IUPAC with Product with Serializable

object C extends UnchargedAminoAcid with Product with Serializable

object CodonGap extends CodonGap with Product with Serializable

object D extends NegativeAminoAcid with Product with Serializable

object DNAtoCodon

object E extends NegativeAminoAcid with Product with Serializable

object F extends HydrophobicAminoAcid with Product with Serializable

object G extends UnchargedAminoAcid with Product with Serializable

object Gap extends Gap with Product with Serializable

object GappedConvert extends GappedConvert[AASymbol]

object GappedDNAtoCodon

object H extends PositiveAminoAcid with Product with Serializable

object I extends HydrophobicAminoAcid with Product with Serializable

object IUPACAminoAcidConvert extends StringConverter[AminoAcid]

object IUPACGappedAminoAcidConvert extends StringConverter[AASymbol]

object IUPACGappedConvert extends GappedConvert[AASymbol]

object K extends PositiveAminoAcid with Product with Serializable

object L extends HydrophobicAminoAcid with Product with Serializable

object M extends HydrophobicAminoAcid with Product with Serializable

object N extends UnchargedAminoAcid with Product with Serializable

object P extends UnchargedAminoAcid with Product with Serializable

object Q extends UnchargedAminoAcid with Product with Serializable

object R extends PositiveAminoAcid with Product with Serializable

object S extends UnchargedAminoAcid with Product with Serializable

object SymbolConvert extends StringConverter[AASymbol]

object T extends UnchargedAminoAcid with Product with Serializable

object U extends UnchargedAminoAcid with Product with Serializable

object V extends HydrophobicAminoAcid with Product with Serializable

object W extends HydrophobicAminoAcid with Product with Serializable

object X extends IUPAC with Product with Serializable

object Y extends HydrophobicAminoAcid with Product with Serializable

object Z extends IUPAC with Product with Serializable

Ungrouped