Uses of Class
com.compomics.util.protein.AASequenceImpl

Packages that use AASequenceImpl

Package	Description
com.compomics.util.gui.spectrum	Spectrum and Chromatogram visualization GUI classes.
com.compomics.util.nucleotide	Useful objects for modeling and handling nucleotides.
com.compomics.util.protein	Classes concerning useful Objects and their operations for modeling and handling proteins.

Uses of AASequenceImpl in com.compomics.util.gui.spectrum

Methods in com.compomics.util.gui.spectrum that return types with arguments of type AASequenceImpl

Modifier and Type	Method	Description
ArrayList<AASequenceImpl>	IsotopicDistributionPanel.getPeptideSequences()	Get the set of peptide sequences.

Uses of AASequenceImpl in com.compomics.util.nucleotide

Methods in com.compomics.util.nucleotide that return AASequenceImpl

Modifier and Type	Method	Description
AASequenceImpl[]	NucleotideSequenceImpl.translate()	This method translates the specified nucleotidesequence into the six reading frames.

Uses of AASequenceImpl in com.compomics.util.protein

Methods in com.compomics.util.protein that return AASequenceImpl

Modifier and Type	Method	Description
AASequenceImpl	AASequenceImpl.getCTermTruncatedSequence(int aTruncationSize)	This method will return an AASequenceImpl that represents a C-terminal truncation of the current sequence.
AASequenceImpl	AASequenceImpl.getNTermTruncatedSequence(int aTruncationSize)	This method will return an AASequenceImpl that represents an N-terminal truncation of the current sequence.
AASequenceImpl	Protein.getSequence()	This method reports on the sequence for the current protein.
AASequenceImpl	AASequenceImpl.getTruncatedSequence(int aStart, int aEnd)	This method will return an AASequenceImpl that represents an internal truncation of the current sequence.
static AASequenceImpl	AASequenceImpl.parsePeptideFromAnnotatedSequence(String aAnnotatedSequence)	This method allows the construction of an AASequenceImpl object, complete with modifications from an annotated sequence String (eg., something like: 'NH2-YS<P>FVATER-COOH' or 'Ace-MATHM<Mox>PIR-COOH').

Methods in com.compomics.util.protein with parameters of type AASequenceImpl

Modifier and Type	Method	Description
void	Protein.setSequence(AASequenceImpl aSequence)	Simple setter for the sequence.

Constructors in com.compomics.util.protein with parameters of type AASequenceImpl

Modifier	Constructor	Description
	Protein(Header aHeader, AASequenceImpl aSequence)	This constructor allows the passing of a Header, as well as an AASequenceImpl for this Protein.
	Protein(Header aHeader, AASequenceImpl aSequence, boolean aTruncated, int aTruncationPosition)	This constructor allows the passing of a Header, as well as an AASequenceImpl for this Protein.
	Protein(AASequenceImpl aSequence)	This constructor requires an AASequenceImpl as argument.