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

Packages that use AminoAcidPattern

Package	Description
com.compomics.util.experiment.biology.aminoacids.sequence	Classes related to the handling of protein sequences.
com.compomics.util.experiment.biology.modifications
com.compomics.util.experiment.identification.protein_sequences.digestion	This package contains classes used to digest protein sequences into peptides.
com.compomics.util.gui	Basic GUI classes.

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

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

Modifier and Type	Method	Description
static AminoAcidPattern	AminoAcidPattern.getAminoAcidPatternFromString(String aminoAcidPatternAsString)	Parses the amino acid pattern from the given string as created by the toString() method.
static AminoAcidPattern	AminoAcidPattern.getAminoAcidPatternFromString(String aminoAcidPatternAsString, int startIndex)	Parses the amino acid pattern from the given string as created by the toString() method.
AminoAcidPattern	AminoAcidPattern.getStandardSearchPattern()	Computes a pattern which can be searched by standard search engines, i.e., a pattern targeting a single amino acid and not a complex pattern.
AminoAcidPattern	AminoAcidPattern.getSubPattern(int startIndex, boolean updateTarget)	Returns a sub pattern of the pattern.
AminoAcidPattern	AminoAcidPattern.getSubPattern(int startIndex, int endIndex, boolean updateTarget)	Returns a sub pattern of the pattern.
static AminoAcidPattern	AminoAcidPattern.getTrypsinExample()	Returns the trypsin example as amino acid pattern.
static AminoAcidPattern	AminoAcidPattern.merge(AminoAcidPattern pattern1, AminoAcidPattern pattern2)	Convenience method merging two different patterns (see public void merge(AminoAcidPattern otherPattern) for detailed information of the merging procedure).
AminoAcidPattern	AminoAcidPattern.reverse()	Returns an amino acid pattern which is a reversed version of the current pattern.

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

Modifier and Type	Method	Description
void	AminoAcidPattern.append(AminoAcidPattern otherPattern)	Appends another pattern at the end of this pattern.
boolean	AminoAcidPattern.contains(AminoAcidPattern aminoAcidPattern, SequenceMatchingParameters sequenceMatchingParameters)	Indicates whether the pattern contains a subsequence of amino acids.
int	AminoAcidPattern.firstIndex(AminoAcidPattern aminoAcidPattern, SequenceMatchingParameters sequenceMatchingParameters)	Returns the first index where the amino acid pattern is found.
int	AminoAcidPattern.firstIndex(AminoAcidPattern aminoAcidPattern, SequenceMatchingParameters sequenceMatchingParameters, int startIndex)	Returns the first index where the amino acid pattern is found in the given pattern.
ArrayList<Integer>	AminoAcidPattern.getIndexes(AminoAcidPattern input, SequenceMatchingParameters sequenceMatchingParameters)	Returns the indexes where the amino acid pattern was found in the input.
boolean	AminoAcidPattern.isEnding(AminoAcidPattern aminoAcidPattern, SequenceMatchingParameters sequenceMatchingParameters)	Indicates whether the given amino acid sequence ends with the pattern.
boolean	AminoAcidPattern.isSameAs(AminoAcidPattern anotherPattern, SequenceMatchingParameters sequenceMatchingParameters)	Indicates whether another AminoAcidPattern targets the same pattern.
boolean	AminoAcidPattern.isStarting(AminoAcidPattern aminoAcidPattern, SequenceMatchingParameters sequenceMatchingParameters)	Indicates whether the given amino acid sequence starts with the pattern.
boolean	AminoAcidPattern.matches(AminoAcidPattern aminoAcidPattern, SequenceMatchingParameters sequenceMatchingParameters)	Indicates whether the pattern matches the given amino acid sequence
boolean	AminoAcidPattern.matchesIn(AminoAcidPattern aminoAcidPattern, SequenceMatchingParameters sequenceMatchingParameters)	Indicates whether the pattern is found in the given amino acid sequence.
void	AminoAcidPattern.merge(AminoAcidPattern otherPattern)	Simple merger for two patterns.
static AminoAcidPattern	AminoAcidPattern.merge(AminoAcidPattern pattern1, AminoAcidPattern pattern2)	Convenience method merging two different patterns (see public void merge(AminoAcidPattern otherPattern) for detailed information of the merging procedure).

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

Modifier	Constructor	Description
	AminoAcidPattern(AminoAcidPattern aminoAcidPattern)	Creates a pattern from another pattern.

Uses of AminoAcidPattern in com.compomics.util.experiment.biology.modifications

Methods in com.compomics.util.experiment.biology.modifications that return AminoAcidPattern

Modifier and Type	Method	Description
AminoAcidPattern	Modification.getPattern()	Returns the amino acid pattern targeted by this modification.

Methods in com.compomics.util.experiment.biology.modifications with parameters of type AminoAcidPattern

Modifier and Type	Method	Description
void	Modification.setPattern(AminoAcidPattern pattern)	Sets the amino acid pattern targeted by this modification.

Constructors in com.compomics.util.experiment.biology.modifications with parameters of type AminoAcidPattern

Modifier	Constructor	Description
	Modification(ModificationType modificationType, String name, String shortName, AtomChain atomChainAdded, AtomChain atomChainRemoved, AminoAcidPattern aminoAcidPattern, ModificationCategory category)	Constructor for a reference modification.
	Modification(ModificationType modificationType, String name, String shortName, AtomChain atomChainAdded, AtomChain atomChainRemoved, AminoAcidPattern aminoAcidPattern, CvTerm unimodCvTerm, CvTerm psiModCvTerm, ModificationCategory category)	Constructor for a reference modification.

Uses of AminoAcidPattern in com.compomics.util.experiment.identification.protein_sequences.digestion

Methods in com.compomics.util.experiment.identification.protein_sequences.digestion that return AminoAcidPattern

Modifier and Type	Method	Description
AminoAcidPattern	ProteinIteratorUtils.getModificationPattern(String modificationName)	Returns the modification pattern that is targeted by the given modification.

Uses of AminoAcidPattern in com.compomics.util.gui

Methods in com.compomics.util.gui that return AminoAcidPattern

Modifier and Type	Method	Description
AminoAcidPattern	AminoAcidPatternDialog.getPattern()	Returns the pattern as edited by the user.

Constructors in com.compomics.util.gui with parameters of type AminoAcidPattern

Modifier	Constructor	Description
	AminoAcidPatternDialog(Frame parent, AminoAcidPattern pattern, boolean editable)	Creates a new AminoAcidPatternDialog.