Package | Description |
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com.compomics.util.gui.spectrum |
Spectrum and Chromatogram visualization GUI classes.
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com.compomics.util.nucleotide |
Useful objects for modeling and handling nucleotides.
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com.compomics.util.protein |
Classes concerning useful Objects and their operations for modeling and handling proteins.
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Modifier and Type | Method and Description |
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ArrayList<AASequenceImpl> |
IsotopicDistributionPanel.getPeptideSequences()
Get the set of peptide sequences.
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Modifier and Type | Method and Description |
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AASequenceImpl[] |
NucleotideSequenceImpl.translate()
This method translates the specified nucleotidesequence into
the six reading frames.
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Modifier and Type | Method and Description |
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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.
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AASequenceImpl |
AASequenceImpl.getTruncatedSequence(int aStart,
int aEnd)
This method will return an AASequenceImpl that represents
an internal truncation of the current sequence.
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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').
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Modifier and Type | Method and Description |
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void |
Protein.setSequence(AASequenceImpl aSequence)
Simple setter for the sequence.
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Constructor and Description |
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Protein(AASequenceImpl aSequence)
This constructor requires an AASequenceImpl as argument.
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Protein(Header aHeader,
AASequenceImpl aSequence)
This constructor allows the passing of a Header, as well as an
AASequenceImpl for this Protein.
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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.
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