Uses of Class
com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence

Packages that use AminoAcidSequence

Package	Description
com.compomics.util.experiment.biology.aminoacids.sequence	Classes related to the handling of protein sequences.
com.compomics.util.experiment.identification.amino_acid_tags	Amino Acid Tag classes.
com.compomics.util.experiment.identification.utils	This package contains utilities classes to handle identification objects.

Uses of AminoAcidSequence in com.compomics.util.experiment.biology.aminoacids.sequence

Methods in com.compomics.util.experiment.biology.aminoacids.sequence that return AminoAcidSequence

Modifier and Type	Method	Description
AminoAcidSequence	AminoAcidSequence.reverse()	Returns an amino acid sequence which is a reversed version of the current pattern.

Methods in com.compomics.util.experiment.biology.aminoacids.sequence with parameters of type AminoAcidSequence

Modifier and Type	Method	Description
void	AminoAcidSequence.appendCTerm(AminoAcidSequence otherSequence)	Appends another sequence at the end of this sequence.
void	AminoAcidSequence.appendNTerm(AminoAcidSequence otherSequence)	Appends another sequence at the beginning of this sequence keeping the original order.
int	AminoAcidPattern.firstIndex(AminoAcidSequence aminoAcidSequence, SequenceMatchingParameters sequenceMatchingParameters)	Returns the first index where the amino acid pattern is found.
void	AminoAcidSequence.insert(int offset, AminoAcidSequence otherSequence)	Inserts another sequence in this sequence.
boolean	AminoAcidSequence.isSameAs(AminoAcidSequence anotherSequence, SequenceMatchingParameters sequenceMatchingPreferences)	Indicates whether another sequence has a matching sequence.
boolean	AminoAcidSequence.isSameSequenceAndModificationStatusAs(AminoAcidSequence anotherSequence, SequenceMatchingParameters sequenceMatchingPreferences)	Indicates whether another sequence targets the same sequence without accounting for PTM localization.
boolean	AminoAcidSequence.matches(AminoAcidSequence aminoAcidSequence, SequenceMatchingParameters sequenceMatchingPreferences)	Indicates whether the sequence matches the given amino acid sequence in size and according to the given matching preferences.
boolean	AminoAcidSequence.matchesIn(AminoAcidSequence aminoAcidSequence, SequenceMatchingParameters sequenceMatchingPreferences)	Indicates whether the sequence is found in the given amino acid sequence.

Constructors in com.compomics.util.experiment.biology.aminoacids.sequence with parameters of type AminoAcidSequence

Modifier	Constructor	Description
	AminoAcidSequence(AminoAcidSequence sequence)	Creates a sequence from another sequence.

Uses of AminoAcidSequence in com.compomics.util.experiment.identification.amino_acid_tags

Methods in com.compomics.util.experiment.identification.amino_acid_tags with parameters of type AminoAcidSequence

Modifier and Type	Method	Description
void	Tag.addAminoAcidSequence(AminoAcidSequence aminoAcidSequence)	Adds a sequence of amino acids to the tag.

Constructors in com.compomics.util.experiment.identification.amino_acid_tags with parameters of type AminoAcidSequence

Modifier	Constructor	Description
	Tag(double nTermGap, AminoAcidSequence sequenceTag, double cTermGap)	Constructor for a tag consisting of a sequence tag between two mass tags.

Uses of AminoAcidSequence in com.compomics.util.experiment.identification.utils

Methods in com.compomics.util.experiment.identification.utils with parameters of type AminoAcidSequence

Modifier and Type	Method	Description
static int[]	ModificationUtils.getPossibleModificationSites(AminoAcidSequence aminoAcidSequence, boolean nTerm, boolean cTerm, Modification modification, SequenceMatchingParameters sequenceMatchingParameters)	Returns an array of the possible modification sites for the given modification on the given peptide.