public class ProteinModificationRegistry
extends java.lang.Object
Constructor | Description |
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ProteinModificationRegistry() |
Modifier and Type | Method | Description |
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static java.util.Set<Component> |
allComponents() |
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static java.util.Set<java.lang.String> |
allIds() |
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static java.util.Set<java.lang.String> |
allKeywords() |
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static java.util.Set<ProteinModification> |
allModifications() |
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static java.util.Set<java.lang.String> |
allPdbccIds() |
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static java.util.Set<java.lang.String> |
allPsimodIds() |
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static java.util.Set<java.lang.String> |
allResidIds() |
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static java.util.Set<ProteinModification> |
getByCategory(ModificationCategory cat) |
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static java.util.Set<ProteinModification> |
getByComponent(Component comp1,
Component... comps) |
Get ProteinModifications that involves one or more components.
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static ProteinModification |
getById(java.lang.String id) |
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static java.util.Set<ProteinModification> |
getByKeyword(java.lang.String keyword) |
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static java.util.Set<ProteinModification> |
getByOccurrenceType(ModificationOccurrenceType occ) |
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static java.util.Set<ProteinModification> |
getByPdbccId(java.lang.String pdbccId) |
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static java.util.Set<ProteinModification> |
getByPsimodId(java.lang.String psimodId) |
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static java.util.Set<ProteinModification> |
getByResidId(java.lang.String residId) |
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static void |
init() |
Initialization the static variables and register common modifications.
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static void |
init(java.io.InputStream inStream) |
Initialization the static variables and register common modifications.
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static void |
register(ProteinModification modification) |
Register a new ProteinModification.
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static void |
unregister(ProteinModification modification) |
Remove a modification from registry.
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public static void init()
public static void init(java.io.InputStream inStream)
inStream
- InputStream to a XML file containing the list of PTMs (as in ptm_list.xml)public static void register(ProteinModification modification)
public static void unregister(ProteinModification modification)
mod
- public static ProteinModification getById(java.lang.String id)
id
- modification ID.public static java.util.Set<ProteinModification> getByResidId(java.lang.String residId)
residId
- RESID ID.public static java.util.Set<ProteinModification> getByPsimodId(java.lang.String psimodId)
psimodId
- PSI-MOD ID.public static java.util.Set<ProteinModification> getByPdbccId(java.lang.String pdbccId)
pdbccId
- Protein Data Bank Chemical Component ID.public static java.util.Set<ProteinModification> getByKeyword(java.lang.String keyword)
keyword
- a keyword.public static java.util.Set<ProteinModification> getByComponent(Component comp1, Component... comps)
public static java.util.Set<ProteinModification> allModifications()
public static java.util.Set<ProteinModification> getByCategory(ModificationCategory cat)
cat
- ModificationCategory
.public static java.util.Set<ProteinModification> getByOccurrenceType(ModificationOccurrenceType occ)
occ
- ModificationOccurrenceType
.public static java.util.Set<java.lang.String> allIds()
public static java.util.Set<java.lang.String> allPdbccIds()
public static java.util.Set<java.lang.String> allResidIds()
public static java.util.Set<java.lang.String> allPsimodIds()
public static java.util.Set<Component> allComponents()
public static java.util.Set<java.lang.String> allKeywords()