Package | Description |
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com.compomics.util.experiment.biology.modifications | |
com.compomics.util.parameters.identification.tool_specific |
Parameters settings for the search algorithms.
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Modifier and Type | Method and Description |
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ModificationCategory |
Modification.getCategory()
Returns the modification category.
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static ModificationCategory |
ModificationCategory.valueOf(String name)
Returns the enum constant of this type with the specified name.
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static ModificationCategory[] |
ModificationCategory.values()
Returns an array containing the constants of this enum type, in
the order they are declared.
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Modifier and Type | Method and Description |
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ArrayList<String> |
ModificationFactory.getModifications(ModificationCategory... modCategories)
Returns the names of all modifications in the given categories.
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void |
Modification.setCategory(ModificationCategory category)
Set the modification category.
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Constructor and Description |
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Modification(ModificationType modificationType,
String name,
Double mass,
ArrayList<String> residues,
ModificationCategory category)
Simple constructor for a modification.
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Modification(ModificationType modificationType,
String name,
String shortName,
AtomChain atomChainAdded,
AtomChain atomChainRemoved,
AminoAcidPattern aminoAcidPattern,
CvTerm unimodCvTerm,
CvTerm psiModCvTerm,
ModificationCategory category)
Constructor for a reference modification.
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Modification(ModificationType modificationType,
String name,
String shortName,
AtomChain atomChainAdded,
AtomChain atomChainRemoved,
AminoAcidPattern aminoAcidPattern,
ModificationCategory category)
Constructor for a reference modification.
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Modifier and Type | Method and Description |
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ArrayList<ModificationCategory> |
MetaMorpheusParameters.getGPtmCategories()
Returns the modification categories to include in the G-PTM search.
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Modifier and Type | Method and Description |
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void |
MetaMorpheusParameters.setGPtmCategories(ArrayList<ModificationCategory> gPtmCategories)
Set the modification categories to include in the G-PTM search.
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