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java.lang.Objectprocope.data.LocalizationData
public class LocalizationData
A set of cellular localization information for proteins.
Colocalization of two proteins means that they share at least one localization in the given data set.
Localizations might be for instance, nuclear, ER, cytoplasmatic etc.
Colocalization
,
LocalizationDataReader
,
ROC.calculateROCCurves(java.util.List, procope.data.complexes.ComplexSet, procope.data.complexes.ComplexSet, LocalizationData, boolean)
Constructor Summary | |
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LocalizationData()
Creates an empty localization data set. |
Method Summary | |
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void |
addLocalization(int protein,
String localization)
Annotate a protein with a given localization. |
byte |
areColocalized(int protein1,
int protein2)
Determines whether two proteins are colocalized. |
String |
getLocalizationName(int id)
Returns the name of a localization for a given internal integer ID |
Collection<Integer> |
getLocalizations(int protein)
Get the set of localizations for a given protein. |
int |
getNumberOfLocalizations()
Returns the number of different localizations in the dataset |
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 LocalizationData()
Method Detail |
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public byte areColocalized(int protein1, int protein2)
protein1
- first proteinprotein2
- second protein
1
if the proteins are colocalized, 0
if they are
not colocalized and -1
if at least one protein has no
localization information and thus colocalization cannot be
determinedpublic Collection<Integer> getLocalizations(int protein)
getLocalizationName(int)
.
protein
- protein for which localizations are retrieved
null
if there are no localization information for
the given proteinpublic String getLocalizationName(int id)
id
- internal integer ID
null
if that internal ID is
not assignedpublic int getNumberOfLocalizations()
public void addLocalization(int protein, String localization)
protein
- protein to be annotatedlocalization
- localization string
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