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Packages that use com.compomics.util.experiment.biology | |
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com.compomics.util.experiment | This package contains MSExperiment main class and all sub-classes useful for the modeling of an experiment. |
com.compomics.util.experiment.biology | This package contains experiement classes related to biological entities. |
com.compomics.util.experiment.biology.aminoacids | |
com.compomics.util.experiment.biology.atoms | |
com.compomics.util.experiment.biology.ions | This package contains experiment classes related to ions. |
com.compomics.util.experiment.biology.neutrallosses | |
com.compomics.util.experiment.identification | This package contains experiment classes related to identifications. |
com.compomics.util.experiment.identification.matches | This package contains experiment classes releated to matches. |
com.compomics.util.experiment.io.identifications | |
com.compomics.util.experiment.quantification.reporterion | This package contains experiment classes related to reporter ions. |
com.compomics.util.gui.spectrum | This package contains GUI classes related to Spectrum and Chromatogram visualization. |
com.compomics.util.protein | The classes in this package concern useful Objects and their operations for modelling and handling proteins. |
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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Atom
This interface contains information about atoms |
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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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FragmentFactory
This factory generates the expected fragment ions from a peptide sequence. |
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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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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. |
Classes in com.compomics.util.experiment.biology used by com.compomics.util.experiment.biology.neutrallosses | |
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NeutralLoss
This class represents a neutral loss. |
Classes in com.compomics.util.experiment.biology used by com.compomics.util.experiment.identification | |
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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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Ion
This class models an ion. |
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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.io.identifications | |
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PTMFactory
This factory will load PTM from an XML file and provide them on demand as standard class. |
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.spectrum | |
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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.protein | |
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Enzyme
This class models an enzyme. |
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