PIP.Collections
Class General

java.lang.Object
  PIP.Collections.General

public class General
extends java.lang.Object

Constructor Summary

General()

Method Summary

static java.util.Map<Pair<Family>,java.util.Collection<DomainInteraction>>	getAtLevel(java.util.Map<Pair<Family>,java.util.Collection<DomainInteraction>> pdbInteractions, FamilyType ft)
static java.util.List<DomainInteraction>	getDomainInteractionsNoXPack(java.util.Collection<DomainInteraction> start)
static java.util.List<DomainInteraction>	getDomainInteractionsWithMaxSize(java.util.Collection<DomainInteraction> domainInteractions, int maxSizeOfList)
static java.util.List<java.util.Map.Entry<Pair<Family>,java.util.Collection<DomainInteraction>>>	getHeterodimersOnlyList(java.util.List<java.util.Map.Entry<Pair<Family>,java.util.Collection<DomainInteraction>>> list, FamilyType ft)
static java.util.List<java.util.Map.Entry<Pair<Family>,java.util.Collection<DomainInteraction>>>	getHomodimersOnlyList(java.util.List<java.util.Map.Entry<Pair<Family>,java.util.Collection<DomainInteraction>>> list, FamilyType ft)
static int	getNumberOfUniqueInteractions(java.util.Collection<DomainInteraction> domainInteractions, FamilyType ft)
static java.util.List<DomainInteraction>	getPDBOnlyInteractions(java.util.List<DomainInteraction> list)
static java.util.List<DomainInteraction>	getProteinOnlyInteractions(java.util.List<DomainInteraction> list)
static boolean	isHomodimer(FamilyType ft, Pair<Family> families)
static java.util.List<DomainInteraction>	removeDuplicatesInSameAssembly(java.util.Collection<DomainInteraction> domainInteractions, FamilyType ft, boolean keepBothPQSAndPDBExample) This makes sure that the PDB interactions are added first and then the PQS interactions that are not in the same assembly as the PDB interactions!
static java.util.List<DomainInteraction>	removeDuplicatesInSameEntry(java.util.Collection<DomainInteraction> domainInteractions, FamilyType ft, boolean keepBothPQSAndPDBExample) This makes sure that the PDB interactions are added first and then the PQS interactions that are not in the same assembly as the PDB interactions!
static java.util.List<DomainInteraction>	removeInteractionsSameAssembly(java.util.List<DomainInteraction> list, FamilyType ft)
static java.util.List<DomainInteraction>	removeInteractionsSameEntry(java.util.List<DomainInteraction> list, FamilyType ft)
static java.util.List<DomainInteraction>	removeInteractionsSameOrientationWithinSameEntry(java.util.List<DomainInteraction> list, FamilyType ft)

Methods inherited from class java.lang.Object

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

Constructor Detail

General

public General()

Method Detail

getHeterodimersOnlyList

public static java.util.List<java.util.Map.Entry<Pair<Family>,java.util.Collection<DomainInteraction>>> getHeterodimersOnlyList(java.util.List<java.util.Map.Entry<Pair<Family>,java.util.Collection<DomainInteraction>>> list,
                                                                                                                                FamilyType ft)
                                                                                                                         throws java.lang.Exception

Parameters:

list -

Returns:

Throws:

java.lang.Exception

getHomodimersOnlyList

public static java.util.List<java.util.Map.Entry<Pair<Family>,java.util.Collection<DomainInteraction>>> getHomodimersOnlyList(java.util.List<java.util.Map.Entry<Pair<Family>,java.util.Collection<DomainInteraction>>> list,
                                                                                                                              FamilyType ft)
                                                                                                                       throws java.lang.Exception

Throws:

java.lang.Exception

isHomodimer

public static boolean isHomodimer(FamilyType ft,
                                  Pair<Family> families)
                           throws java.lang.Exception

Throws:

java.lang.Exception

getPDBOnlyInteractions

public static java.util.List<DomainInteraction> getPDBOnlyInteractions(java.util.List<DomainInteraction> list)

getProteinOnlyInteractions

public static java.util.List<DomainInteraction> getProteinOnlyInteractions(java.util.List<DomainInteraction> list)

getDomainInteractionsNoXPack

public static java.util.List<DomainInteraction> getDomainInteractionsNoXPack(java.util.Collection<DomainInteraction> start)

removeInteractionsSameOrientationWithinSameEntry

public static java.util.List<DomainInteraction> removeInteractionsSameOrientationWithinSameEntry(java.util.List<DomainInteraction> list,
                                                                                                 FamilyType ft)

removeInteractionsSameAssembly

public static java.util.List<DomainInteraction> removeInteractionsSameAssembly(java.util.List<DomainInteraction> list,
                                                                               FamilyType ft)

removeInteractionsSameEntry

public static java.util.List<DomainInteraction> removeInteractionsSameEntry(java.util.List<DomainInteraction> list,
                                                                            FamilyType ft)

getAtLevel

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

Throws:

java.lang.Exception

getDomainInteractionsWithMaxSize

public static java.util.List<DomainInteraction> getDomainInteractionsWithMaxSize(java.util.Collection<DomainInteraction> domainInteractions,
                                                                                 int maxSizeOfList)

removeDuplicatesInSameAssembly

public static java.util.List<DomainInteraction> removeDuplicatesInSameAssembly(java.util.Collection<DomainInteraction> domainInteractions,
                                                                               FamilyType ft,
                                                                               boolean keepBothPQSAndPDBExample)
                                                                        throws java.lang.Exception

This makes sure that the PDB interactions are added first and then the PQS interactions that are not in the same assembly as the PDB interactions!

Parameters:

domainInteractions -

ft -

keepBothPQSAndPDBExample -

Returns:

Throws:

java.lang.Exception

removeDuplicatesInSameEntry

public static java.util.List<DomainInteraction> removeDuplicatesInSameEntry(java.util.Collection<DomainInteraction> domainInteractions,
                                                                            FamilyType ft,
                                                                            boolean keepBothPQSAndPDBExample)
                                                                     throws java.lang.Exception

This makes sure that the PDB interactions are added first and then the PQS interactions that are not in the same assembly as the PDB interactions!

Parameters:

domainInteractions -

ft -

keepBothPQSAndPDBExample -

Returns:

Throws:

java.lang.Exception

getNumberOfUniqueInteractions

public static int getNumberOfUniqueInteractions(java.util.Collection<DomainInteraction> domainInteractions,
                                                FamilyType ft)
                                         throws java.lang.Exception

Throws:

java.lang.Exception