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

Packages that use AASequenceImpl
com.compomics.util.gui.spectrum This package contains GUI classes related to Spectrum and Chromatogram visualization. 
com.compomics.util.nucleotide The classes in this package concern useful Objects and their operations for modelling and handling nucleotides. 
com.compomics.util.protein The classes in this package concern useful Objects and their operations for modelling 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
 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
 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
 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-YSFVATER-COOH' or 'Ace-MATHMPIR-COOH').
 

Methods in com.compomics.util.protein with parameters of type AASequenceImpl
 void Protein.setSequence(AASequenceImpl aSequence)
          Simple setter for the sequence.
 

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



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