com.compomics.util.pride

Class PrideObjectsFactory

java.lang.Object

com.compomics.util.pride.PrideObjectsFactory

public class PrideObjectsFactory
extends Object

This factory manages the pride objects saved in the user folder.

Author:

Marc Vaudel

Field Summary

Fields

Modifier and Type	Field and Description
static String	extension The extension to use when saving objects.

Method Summary

Modifier and Type	Method and Description
void	addContactGroup(ContactGroup contactGroup) Adds a contact group in the PRIDE objects.
void	addInstrument(Instrument instrument) Adds a instrument in the PRIDE objects.
void	addProtocol(Protocol protocol) Adds a protocol in the PRIDE objects.
void	addReferenceGroup(ReferenceGroup referenceGroup) Adds a reference group in the PRIDE objects.
void	addSample(Sample sample) Adds a sample in the PRIDE objects.
void	deleteContactGroup(ContactGroup contactGroup) Delete the given contact group.
void	deleteInstrument(Instrument instrument) Delete the given instrument.
void	deleteProtocol(Protocol protocol) Delete the given protocol.
void	deleteReferenceGroup(ReferenceGroup referenceGroup) Delete the given reference group.
void	deleteSample(Sample sample) Delete the given sample.
HashMap<String,ContactGroup>	getContactGroups() Returns the contact groups.
static PrideObjectsFactory	getInstance() Method returning the instance of the factory.
HashMap<String,Instrument>	getInstruments() Returns the instruments.
static String	getPrideFolder() Returns the folder where pride annotation information should be saved.
HashMap<String,Protocol>	getProtocols() Returns the protocols.
PtmToPrideMap	getPtmToPrideMap() Returns the utilities PTM to pride map.
HashMap<String,ReferenceGroup>	getReferenceGroups() Returns the reference groups.
HashMap<String,Sample>	getSamples() Returns the samples.
static void	setPrideFolder(String prideFolder) Sets the folder where pride annotation information should be saved.
void	setPtmToPrideMap(PtmToPrideMap ptmToPrideMap) Sets a new PTM to PRIDE map.

Methods inherited from class java.lang.Object

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

Field Detail

extension

public static final String extension

The extension to use when saving objects. By default cus for compomics utilities serialization

See Also:

Constant Field Values

Method Detail

getInstance

public static PrideObjectsFactory getInstance()
                                       throws FileNotFoundException,
                                              IOException,
                                              ClassNotFoundException

Method returning the instance of the factory.

Returns:

the instance of the factory

Throws:

FileNotFoundException - exception thrown whenever the file was not found

IOException - exception thrown whenever an error occurred while writing the file

ClassNotFoundException - exception thrown whenever an error occurred while serializing the file

addContactGroup

public void addContactGroup(ContactGroup contactGroup)
                     throws IOException

Adds a contact group in the PRIDE objects.

Parameters:

contactGroup - the contact group to add

Throws:

IOException - exception thrown whenever an error occurred while saving

deleteContactGroup

public void deleteContactGroup(ContactGroup contactGroup)

Delete the given contact group.

Parameters:

contactGroup - the group to delete

addProtocol

public void addProtocol(Protocol protocol)
                 throws IOException

Adds a protocol in the PRIDE objects.

Parameters:

protocol - the protocol to add

Throws:

IOException - exception thrown whenever an error occurred while saving

deleteProtocol

public void deleteProtocol(Protocol protocol)

Delete the given protocol.

Parameters:

protocol - the protocol to delete

addInstrument

public void addInstrument(Instrument instrument)
                   throws IOException

Adds a instrument in the PRIDE objects.

Parameters:

instrument - the instrument to add

Throws:

IOException - exception thrown whenever an error occurred while saving

deleteInstrument

public void deleteInstrument(Instrument instrument)

Delete the given instrument.

Parameters:

instrument - the instrument to delete

addReferenceGroup

public void addReferenceGroup(ReferenceGroup referenceGroup)
                       throws IOException

Adds a reference group in the PRIDE objects.

Parameters:

referenceGroup - the reference group to add

Throws:

IOException - exception thrown whenever an error occurred while saving

deleteReferenceGroup

public void deleteReferenceGroup(ReferenceGroup referenceGroup)

Delete the given reference group.

Parameters:

referenceGroup - the reference group to delete

addSample

public void addSample(Sample sample)
               throws IOException

Adds a sample in the PRIDE objects.

Parameters:

sample - the sample to add

Throws:

IOException - exception thrown whenever an error occurred while saving

deleteSample

public void deleteSample(Sample sample)

Delete the given sample.

Parameters:

sample - the sample to delete

setPtmToPrideMap

public void setPtmToPrideMap(PtmToPrideMap ptmToPrideMap)
                      throws FileNotFoundException,
                             IOException

Sets a new PTM to PRIDE map.

Parameters:

ptmToPrideMap - a new PTM to pride map

Throws:

FileNotFoundException - if a FileNotFoundException occurs

IOException - if an IOException occurs

getContactGroups

public HashMap<String,ContactGroup> getContactGroups()

Returns the contact groups.

Returns:

the contact groups

getInstruments

public HashMap<String,Instrument> getInstruments()

Returns the instruments.

Returns:

the instruments

getProtocols

public HashMap<String,Protocol> getProtocols()

Returns the protocols.

Returns:

the protocols

getPtmToPrideMap

public PtmToPrideMap getPtmToPrideMap()

Returns the utilities PTM to pride map.

Returns:

the utilities PTM to pride map

getReferenceGroups

public HashMap<String,ReferenceGroup> getReferenceGroups()

Returns the reference groups.

Returns:

the reference groups

getSamples

public HashMap<String,Sample> getSamples()

Returns the samples.

Returns:

the samples

getPrideFolder

public static String getPrideFolder()

Returns the folder where pride annotation information should be saved.

Returns:

the folder where pride annotation information should be saved

setPrideFolder

public static void setPrideFolder(String prideFolder)

Sets the folder where pride annotation information should be saved.

Parameters:

prideFolder - the folder where pride annotation information should be saved