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java.lang.Objectdata.purifications.PurificationData
public class PurificationData
A set of protein purification experiments where each experiment constists of a bait protein along with a list of prey proteins it purified.
The score calculation methods in this library are based on such
collections of purification experiments and require a PurificationData
object as an input.
This class is a simple container method with basic accession and some data manipulation methods.
PurificationExperiment
,
PurificationDataReader
,
SocioAffinityCalculator
,
PECalculator
,
HartCalculator
,
Bootstrap
Constructor Summary | |
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PurificationData()
Creates an empty purification dataset |
Method Summary | |
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void |
addExperiment(PurificationExperiment experiment)
Adds a specified experiment to the dataset. |
void |
addExperiments(Collection<PurificationExperiment> experiments)
Adds a list of purification experiments to the dataset |
ProteinNetwork |
getBaitPreyInteractions()
Calculates a directed network containing all bait-prey interactions. |
List<PurificationExperiment> |
getExperiments()
Returns the list of PurificationExperiment objects backing this dataset. |
int |
getNumberOfExperiments()
Returns the number of experiments contained in this dataset |
int |
getPreyCount()
Returns the total number of preys in this dataset. |
Set<Integer> |
getProteins()
Returns the set of proteins which are contained in this purification data set |
Iterator<PurificationExperiment> |
iterator()
Returns an iterator over all purification experiments in this dataset. |
PurificationData |
merge(PurificationData mergeWith)
Merges two purification datasets. |
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 PurificationData()
Method Detail |
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public List<PurificationExperiment> getExperiments()
PurificationData
object.
public void addExperiment(PurificationExperiment experiment)
experiment
- the experiment to be addedpublic void addExperiments(Collection<PurificationExperiment> experiments)
experiments
- list of experiments to be addedpublic int getNumberOfExperiments()
public ProteinNetwork getBaitPreyInteractions()
public Set<Integer> getProteins()
getProteins
in interface ProteinSet
public int getPreyCount()
public Iterator<PurificationExperiment> iterator()
iterator
in interface Iterable<PurificationExperiment>
public PurificationData merge(PurificationData mergeWith)
mergeWith
- other purification data set this one will be merged with
PurificationData
object containing the
purification experiments of both source datasets
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