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