PIP.Domains.Interactions
Class DomainInteractions

java.lang.Object
  PIP.Domains.Interactions.DomainInteractions

public class DomainInteractions
extends java.lang.Object

Constructor Summary

DomainInteractions(boolean b)
The great thing about the domain interactions which are stored is that they only contain interactions that are protein-protein interactions and not due to crystal packing.

Method Summary

java.util.Map<Family,java.util.Collection<DomainInteraction>>	getDomainInteractionsHashedByFamily(FamilyType ft)
java.util.Map<Pair<Family>,java.util.Collection<DomainInteraction>>	getDomainInteractionsHashedByFamilyPair(FamilyType ft)
java.util.Map<FamilyType,java.util.Map<Family,java.util.Collection<DomainInteraction>>>	getFamilyMap()
java.util.Map<FamilyType,java.util.Map<Pair<Family>,java.util.Collection<DomainInteraction>>>	getfamilyPairMap()
static DomainInteractions	getInstance()
java.util.Collection<DomainInteraction>	getUniqueDomainInteractionsForFamily(FamilyType ft, java.util.Comparator comp)
java.util.Collection<DomainInteraction>	getUniqueDomainInteractionsForFamilyPair(FamilyType ft, java.util.Comparator comp) This is a useful class to get a non redundant set of Domain Interactions for any Family Type and level of similarity.
static void	orderMapByFamilyTypeLevel(java.util.Map.Entry<Pair<Family>,java.util.Collection<DomainInteraction>> me, FamilyType ft, java.util.Map<Pair<Family>,java.util.Collection<DomainInteraction>> map)
void	persistFamilyToDomainInteractions(FamilyType ft)
void	persistPairFamilyToDomainInteractions(FamilyType ft)

Methods inherited from class java.lang.Object

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

Constructor Detail

DomainInteractions

public DomainInteractions(boolean b)

The great thing about the domain interactions which are stored is that they only contain interactions that are protein-protein interactions and not due to crystal packing.

Parameters:

b -

Method Detail

getfamilyPairMap

public java.util.Map<FamilyType,java.util.Map<Pair<Family>,java.util.Collection<DomainInteraction>>> getfamilyPairMap()

getFamilyMap

public java.util.Map<FamilyType,java.util.Map<Family,java.util.Collection<DomainInteraction>>> getFamilyMap()

getInstance

public static DomainInteractions getInstance()

getDomainInteractionsHashedByFamilyPair

public java.util.Map<Pair<Family>,java.util.Collection<DomainInteraction>> getDomainInteractionsHashedByFamilyPair(FamilyType ft)
                                                                                                            throws java.lang.Exception

Throws:

java.lang.Exception

orderMapByFamilyTypeLevel

public static void orderMapByFamilyTypeLevel(java.util.Map.Entry<Pair<Family>,java.util.Collection<DomainInteraction>> me,
                                             FamilyType ft,
                                             java.util.Map<Pair<Family>,java.util.Collection<DomainInteraction>> map)
                                      throws java.lang.Exception

Throws:

java.lang.Exception

getDomainInteractionsHashedByFamily

public java.util.Map<Family,java.util.Collection<DomainInteraction>> getDomainInteractionsHashedByFamily(FamilyType ft)
                                                                                                  throws java.lang.Exception

Throws:

java.lang.Exception

getUniqueDomainInteractionsForFamilyPair

public java.util.Collection<DomainInteraction> getUniqueDomainInteractionsForFamilyPair(FamilyType ft,
                                                                                        java.util.Comparator comp)
                                                                                 throws java.lang.Exception

This is a useful class to get a non redundant set of Domain Interactions for any Family Type and level of similarity. For example pass in a HFType of SCOP at level 3 and a highest resolution comparitor to return the highest resolution domain interaction for each superfamily.

Parameters:

ft -

comp -

Returns:

A collection of non-redundant domain interactions for the inputted level of ft

Throws:

java.lang.Exception

getUniqueDomainInteractionsForFamily

public java.util.Collection<DomainInteraction> getUniqueDomainInteractionsForFamily(FamilyType ft,
                                                                                    java.util.Comparator comp)
                                                                             throws java.lang.Exception

Throws:

java.lang.Exception

persistPairFamilyToDomainInteractions

public void persistPairFamilyToDomainInteractions(FamilyType ft)
                                           throws java.lang.Exception

Throws:

java.lang.Exception

persistFamilyToDomainInteractions

public void persistFamilyToDomainInteractions(FamilyType ft)
                                       throws java.lang.Exception

Throws:

java.lang.Exception