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Classes in com.compomics.util.experiment.biology used by com.compomics.util.experiment | |
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Sample
This class models a proteomic sample. |
Classes in com.compomics.util.experiment.biology used by com.compomics.util.experiment.biology | |
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AminoAcid
Class representing amino acids. |
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AminoAcidPattern
An amino acid pattern is a sequence of amino-acids. |
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Atom
This interface contains information about atoms |
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ElementaryElement
This class can be used to retrieve elementary elements like a neutron. |
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Enzyme
This class models an enzyme. |
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EnzymeFactory
This factory will provide the implemented enzymes. |
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GlyconFactory
This factory will provide theoretic glycons. |
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Ion
This class models an ion. |
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Ion.IonType
An enumerator of the supported ion types. |
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IonFactory
This factory generates the expected ions from a peptide. |
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Mutation
This class represents a mutation of one amino acid to another from the 20-letter amino acid alphabet. |
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NeutralLoss
This class represents a neutral loss. |
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Peptide
This class models a peptide. |
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Protein
This class models a protein. |
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PTM
This class models a post-translational modification. |
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PTMFactory
This factory will load PTM from an XML file and provide them on demand as standard class. |
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Sample
This class models a proteomic sample. |
Classes in com.compomics.util.experiment.biology used by com.compomics.util.experiment.biology.aminoacids | |
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AminoAcid
Class representing amino acids. |
Classes in com.compomics.util.experiment.biology used by com.compomics.util.experiment.biology.atoms | |
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Atom
This interface contains information about atoms |
Classes in com.compomics.util.experiment.biology used by com.compomics.util.experiment.biology.ions | |
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Ion
This class models an ion. |
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NeutralLoss
This class represents a neutral loss. |
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Peptide
This class models a peptide. |
Classes in com.compomics.util.experiment.biology used by com.compomics.util.experiment.identification | |
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Enzyme
This class models an enzyme. |
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Ion
This class models an ion. |
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Ion.IonType
An enumerator of the supported ion types. |
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NeutralLoss
This class represents a neutral loss. |
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Peptide
This class models a peptide. |
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Protein
This class models a protein. |
Classes in com.compomics.util.experiment.biology used by com.compomics.util.experiment.identification.matches | |
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Enzyme
This class models an enzyme. |
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Ion
This class models an ion. |
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Peptide
This class models a peptide. |
Classes in com.compomics.util.experiment.biology used by com.compomics.util.experiment.identification.protein_inference.proteintree | |
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Enzyme
This class models an enzyme. |
Classes in com.compomics.util.experiment.biology used by com.compomics.util.experiment.identification.ptm | |
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Ion.IonType
An enumerator of the supported ion types. |
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Peptide
This class models a peptide. |
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PTM
This class models a post-translational modification. |
Classes in com.compomics.util.experiment.biology used by com.compomics.util.experiment.identification.ptm.ptmscores | |
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Ion.IonType
An enumerator of the supported ion types. |
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Peptide
This class models a peptide. |
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PTM
This class models a post-translational modification. |
Classes in com.compomics.util.experiment.biology used by com.compomics.util.experiment.identification.scoring | |
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Ion.IonType
An enumerator of the supported ion types. |
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Peptide
This class models a peptide. |
Classes in com.compomics.util.experiment.biology used by com.compomics.util.experiment.quantification.reporterion | |
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Sample
This class models a proteomic sample. |
Classes in com.compomics.util.experiment.biology used by com.compomics.util.gui | |
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AminoAcidPattern
An amino acid pattern is a sequence of amino-acids. |
Classes in com.compomics.util.experiment.biology used by com.compomics.util.gui.ptm | |
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PTM
This class models a post-translational modification. |
Classes in com.compomics.util.experiment.biology used by com.compomics.util.gui.searchsettings | |
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Enzyme
This class models an enzyme. |
Classes in com.compomics.util.experiment.biology used by com.compomics.util.gui.spectrum | |
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Ion
This class models an ion. |
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Ion.IonType
An enumerator of the supported ion types. |
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NeutralLoss
This class represents a neutral loss. |
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Peptide
This class models a peptide. |
Classes in com.compomics.util.experiment.biology used by com.compomics.util.preferences | |
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Ion.IonType
An enumerator of the supported ion types. |
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NeutralLoss
This class represents a neutral loss. |
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Peptide
This class models a peptide. |
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PTM
This class models a post-translational modification. |
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