public class PrideObjectsFactory
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
static java.lang.String |
extension
The extension to use when saving objects.
|
static java.lang.String |
prideFolder
The folder where PRIDE related info is stored.
|
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.
|
java.util.HashMap<java.lang.String,ContactGroup> |
getContactGroups()
Returns the contact groups.
|
static PrideObjectsFactory |
getInstance()
Method returning the instance of the factory.
|
java.util.HashMap<java.lang.String,Instrument> |
getInstruments()
Returns the instruments.
|
java.util.HashMap<java.lang.String,Protocol> |
getProtocols()
Returns the protocols.
|
PtmToPrideMap |
getPtmToPrideMap()
Returns the utilities ptm to pride map.
|
java.util.HashMap<java.lang.String,ReferenceGroup> |
getReferenceGroups()
Returns the reference groups.
|
java.util.HashMap<java.lang.String,Sample> |
getSamples()
Returns the samples.
|
void |
setPtmToPrideMap(PtmToPrideMap ptmToPrideMap)
Sets a new ptm to PRIDE map.
|
public static final java.lang.String prideFolder
public static final java.lang.String extension
public static PrideObjectsFactory getInstance() throws java.io.FileNotFoundException, java.io.IOException, java.lang.ClassNotFoundException
java.io.FileNotFoundException
- exception thrown whenever the file was not
foundjava.io.IOException
- exception thrown whenever an error occurred while
writing the filejava.lang.ClassNotFoundException
- exception thrown whenever an error
occurred while serializing the filepublic void addContactGroup(ContactGroup contactGroup) throws java.io.IOException
contactGroup
- the contact group to addjava.io.IOException
- exception thrown whenever an error occurred while
savingpublic void deleteContactGroup(ContactGroup contactGroup)
contactGroup
- the group to deletepublic void addProtocol(Protocol protocol) throws java.io.IOException
protocol
- the protocol to addjava.io.IOException
- exception thrown whenever an error occurred while
savingpublic void deleteProtocol(Protocol protocol)
protocol
- the protocol to deletepublic void addInstrument(Instrument instrument) throws java.io.IOException
instrument
- the instrument to addjava.io.IOException
- exception thrown whenever an error occurred while
savingpublic void deleteInstrument(Instrument instrument)
instrument
- the instrument to deletepublic void addReferenceGroup(ReferenceGroup referenceGroup) throws java.io.IOException
referenceGroup
- the reference group to addjava.io.IOException
- exception thrown whenever an error occurred while
savingpublic void deleteReferenceGroup(ReferenceGroup referenceGroup)
referenceGroup
- the reference group to deletepublic void addSample(Sample sample) throws java.io.IOException
sample
- the sample to addjava.io.IOException
- exception thrown whenever an error occurred while
savingpublic void deleteSample(Sample sample)
sample
- the sample to deletepublic void setPtmToPrideMap(PtmToPrideMap ptmToPrideMap) throws java.io.FileNotFoundException, java.io.IOException
ptmToPrideMap
- a new ptm to pride mapjava.io.FileNotFoundException
java.io.IOException
public java.util.HashMap<java.lang.String,ContactGroup> getContactGroups()
public java.util.HashMap<java.lang.String,Instrument> getInstruments()
public java.util.HashMap<java.lang.String,Protocol> getProtocols()
public PtmToPrideMap getPtmToPrideMap()
public java.util.HashMap<java.lang.String,ReferenceGroup> getReferenceGroups()
public java.util.HashMap<java.lang.String,Sample> getSamples()
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