Package org.biojava.nbio.protmod
Class ProteinModificationRegistry
- java.lang.Object
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- org.biojava.nbio.protmod.ProteinModificationRegistry
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public class ProteinModificationRegistry extends java.lang.Object
This class serves as a instance registry by maintaining a pool of ProteinModification instances. A list of common protein modifications were preloaded from an XML file.- Since:
- 3.0
- Author:
- Jianjiong Gao
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Constructor Summary
Constructors Constructor Description ProteinModificationRegistry()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static java.util.Set<Component>
allComponents()
static java.util.Set<java.lang.String>
allIds()
static java.util.Set<java.lang.String>
allKeywords()
static java.util.Set<ProteinModification>
allModifications()
static java.util.Set<java.lang.String>
allPdbccIds()
static java.util.Set<java.lang.String>
allPsimodIds()
static java.util.Set<java.lang.String>
allResidIds()
static java.util.Set<ProteinModification>
getByCategory(ModificationCategory cat)
static java.util.Set<ProteinModification>
getByComponent(Component comp1, Component... comps)
Get ProteinModifications that involves one or more components.static ProteinModification
getById(java.lang.String id)
static java.util.Set<ProteinModification>
getByKeyword(java.lang.String keyword)
static java.util.Set<ProteinModification>
getByOccurrenceType(ModificationOccurrenceType occ)
static java.util.Set<ProteinModification>
getByPdbccId(java.lang.String pdbccId)
static java.util.Set<ProteinModification>
getByPsimodId(java.lang.String psimodId)
static java.util.Set<ProteinModification>
getByResidId(java.lang.String residId)
static void
init()
Initialization the static variables and register common modifications.static void
init(java.io.InputStream inStream)
Initialization the static variables and register common modifications.static void
register(ProteinModification modification)
Register a new ProteinModification.static void
unregister(ProteinModification modification)
Remove a modification from registry.
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Method Detail
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init
public static void init()
Initialization the static variables and register common modifications.
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init
public static void init(java.io.InputStream inStream)
Initialization the static variables and register common modifications. Allows external user to provide alternative ptm_list.xml file instead of the one contained in this jar file.- Parameters:
inStream
- InputStream to a XML file containing the list of PTMs (as in ptm_list.xml)
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register
public static void register(ProteinModification modification)
Register a new ProteinModification.
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unregister
public static void unregister(ProteinModification modification)
Remove a modification from registry.- Parameters:
mod
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getById
public static ProteinModification getById(java.lang.String id)
- Parameters:
id
- modification ID.- Returns:
- ProteinModification that has the corresponding ID.
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getByResidId
public static java.util.Set<ProteinModification> getByResidId(java.lang.String residId)
- Parameters:
residId
- RESID ID.- Returns:
- a set of ProteinModifications that have the RESID ID.
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getByPsimodId
public static java.util.Set<ProteinModification> getByPsimodId(java.lang.String psimodId)
- Parameters:
psimodId
- PSI-MOD ID.- Returns:
- a set of ProteinModifications that have the PSI-MOD ID.
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getByPdbccId
public static java.util.Set<ProteinModification> getByPdbccId(java.lang.String pdbccId)
- Parameters:
pdbccId
- Protein Data Bank Chemical Component ID.- Returns:
- a set of ProteinModifications that have the PDBCC ID.
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getByKeyword
public static java.util.Set<ProteinModification> getByKeyword(java.lang.String keyword)
- Parameters:
keyword
- a keyword.- Returns:
- a set of ProteinModifications that have the keyword.
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getByComponent
public static java.util.Set<ProteinModification> getByComponent(Component comp1, Component... comps)
Get ProteinModifications that involves one or more components.
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allModifications
public static java.util.Set<ProteinModification> allModifications()
- Returns:
- set of all registered ProteinModifications.
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getByCategory
public static java.util.Set<ProteinModification> getByCategory(ModificationCategory cat)
- Parameters:
cat
-ModificationCategory
.- Returns:
- set of registered ProteinModifications in a particular category.
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getByOccurrenceType
public static java.util.Set<ProteinModification> getByOccurrenceType(ModificationOccurrenceType occ)
- Parameters:
occ
-ModificationOccurrenceType
.- Returns:
- set of registered ProteinModifications of a particular occurrence type.
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allIds
public static java.util.Set<java.lang.String> allIds()
- Returns:
- set of IDs of all registered ProteinModifications.
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allPdbccIds
public static java.util.Set<java.lang.String> allPdbccIds()
- Returns:
- set of PDBCC IDs of all registered ProteinModifications.
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allResidIds
public static java.util.Set<java.lang.String> allResidIds()
- Returns:
- set of RESID IDs of all registered ProteinModifications.
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allPsimodIds
public static java.util.Set<java.lang.String> allPsimodIds()
- Returns:
- set of PSI-MOD IDs of all registered ProteinModifications.
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allComponents
public static java.util.Set<Component> allComponents()
- Returns:
- set of components involved in all registered ProteinModifications.
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allKeywords
public static java.util.Set<java.lang.String> allKeywords()
- Returns:
- set of keywords of all registered ProteinModifications.
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