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java.lang.Objectorg.biojava3.protmod.ProteinModificationRegistry
public class ProteinModificationRegistry
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.
Constructor Summary | |
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ProteinModificationRegistry()
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Method Summary | |
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static Set<Component> |
allComponents()
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static Set<String> |
allIds()
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static Set<String> |
allKeywords()
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static Set<ProteinModification> |
allModifications()
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static Set<String> |
allPdbccIds()
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static Set<String> |
allPsimodIds()
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static Set<String> |
allResidIds()
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static Set<ProteinModification> |
getByCategory(ModificationCategory cat)
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static Set<ProteinModification> |
getByComponent(Component comp1,
Component... comps)
Get ProteinModifications that involves one or more components. |
static ProteinModification |
getById(String id)
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static Set<ProteinModification> |
getByKeyword(String keyword)
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static Set<ProteinModification> |
getByOccurrenceType(ModificationOccurrenceType occ)
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static Set<ProteinModification> |
getByPdbccId(String pdbccId)
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static Set<ProteinModification> |
getByPsimodId(String psimodId)
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static Set<ProteinModification> |
getByResidId(String residId)
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static void |
init()
Initialization the static variables and register common modifications. |
static void |
init(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. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public ProteinModificationRegistry()
Method Detail |
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public static void init()
public static void init(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(String id)
id
- modification ID.
public static Set<ProteinModification> getByResidId(String residId)
residId
- RESID ID.
public static Set<ProteinModification> getByPsimodId(String psimodId)
psimodId
- PSI-MOD ID.
public static Set<ProteinModification> getByPdbccId(String pdbccId)
pdbccId
- Protein Data Bank Chemical Component ID.
public static Set<ProteinModification> getByKeyword(String keyword)
keyword
- a keyword.
public static Set<ProteinModification> getByComponent(Component comp1, Component... comps)
comp1
- a Component
.comps
- other Component
s.
public static Set<ProteinModification> allModifications()
public static Set<ProteinModification> getByCategory(ModificationCategory cat)
cat
- ModificationCategory
.
public static Set<ProteinModification> getByOccurrenceType(ModificationOccurrenceType occ)
occ
- ModificationOccurrenceType
.
public static Set<String> allIds()
public static Set<String> allPdbccIds()
public static Set<String> allResidIds()
public static Set<String> allPsimodIds()
public static Set<Component> allComponents()
public static Set<String> allKeywords()
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