com.compomics.util.experiment

Class MsExperiment

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

com.compomics.util.experiment.MsExperiment

All Implemented Interfaces:

Serializable, Cloneable

public class MsExperiment
extends ExperimentObject

This class represents the experiment.

Author:

Marc Vaudel

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static String	experimentObjectName The name of the serialized experiment.

Constructor Summary

Constructors

Constructor and Description
MsExperiment(String reference) Constructor for an experiment.
MsExperiment(String reference, HashMap<Integer,Sample> samples) Constructor for an experiment.

Method Summary

Modifier and Type	Method and Description
void	addAnalysisSet(Sample sample, SampleAnalysisSet analysisSet) Method to link an analysis set to an experiment.
SampleAnalysisSet	getAnalysisSet(Sample sample) Returns the analysis set corresponding to a sample.
String	getReference() Returns the reference of the experiment.
Sample	getSample(int id) Returns a single sample accessed by its index.
HashMap<Integer,Sample>	getSamples() Returns the implemented samples.
void	setReference(String reference) Sets the reference of the experiment.
void	setSample(int index, Sample sample) Set a new sample.

Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject

addUrParam, getParameterKey, getUrParam

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

experimentObjectName

public static final String experimentObjectName

The name of the serialized experiment.

See Also:

Constant Field Values

Constructor Detail

MsExperiment

public MsExperiment(String reference,
                    HashMap<Integer,Sample> samples)

Constructor for an experiment.

Parameters:

reference - the reference of the experiment

samples - the samples analyzed

MsExperiment

public MsExperiment(String reference)

Constructor for an experiment.

Parameters:

reference - the reference of the experiment

Method Detail

getReference

public String getReference()

Returns the reference of the experiment.

Returns:

reference of the experiment

setReference

public void setReference(String reference)

Sets the reference of the experiment.

Parameters:

reference - the experiment reference

addAnalysisSet

public void addAnalysisSet(Sample sample,
                           SampleAnalysisSet analysisSet)

Method to link an analysis set to an experiment.

Parameters:

sample - the reference sample

analysisSet - the analysis set corresponding to this sample

getAnalysisSet

public SampleAnalysisSet getAnalysisSet(Sample sample)

Returns the analysis set corresponding to a sample.

Parameters:

sample - the reference sample

Returns:

the analysis set corresponding to the reference sample

getSamples

public HashMap<Integer,Sample> getSamples()

Returns the implemented samples.

Returns:

map containing all samples

getSample

public Sample getSample(int id)

Returns a single sample accessed by its index.

Parameters:

id - the index of the desired sample

Returns:

the desired sample

setSample

public void setSample(int index,
                      Sample sample)

Set a new sample.

Parameters:

index - the index of the sample

sample - the new sample