PIP.Domains.SequenceSimilarity
Class SequenceClassifiedDIs

java.lang.Object
  PIP.Domains.SequenceSimilarity.SequenceClassifiedDIs

public class SequenceClassifiedDIs
extends java.lang.Object

Constructor Summary

SequenceClassifiedDIs()

Method Summary

static void	classifyInteractionsIntoThoseWithSameSequence(java.util.List<java.util.List<DomainInteraction>> sameList, java.util.List<DomainInteraction> startingList, int percentage)
static boolean	domainsHaveSameSequence(DomainInteraction di0, DomainInteraction di1, int percentage)
static java.util.Map<Pair<Family>,java.util.Collection<java.util.List<DomainInteraction>>>	getDomainInteractionsHashedByFamilyPair(java.util.Map<Pair<Family>,java.util.Collection<DomainInteraction>> map, int counter, int start, int end, int percentage) This classifies all the interactions into those with the same sequence ie two domain interactions have the same pairwise sequences A->A' is same sequence and B->B' is same sequence - not is one domain interaction a homodimer.
static java.util.List<java.util.List<DomainInteraction>>	getSequenceSimilarInteractions(java.util.Collection<DomainInteraction> familyClassifiedInteractions, int percentage)
static boolean	isSequenceLevelHomodimer(java.util.Collection<DomainInteraction> domainInteractions, int percentage)

Methods inherited from class java.lang.Object

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

Constructor Detail

SequenceClassifiedDIs

public SequenceClassifiedDIs()

Method Detail

getDomainInteractionsHashedByFamilyPair

public static java.util.Map<Pair<Family>,java.util.Collection<java.util.List<DomainInteraction>>> getDomainInteractionsHashedByFamilyPair(java.util.Map<Pair<Family>,java.util.Collection<DomainInteraction>> map,
                                                                                                                                          int counter,
                                                                                                                                          int start,
                                                                                                                                          int end,
                                                                                                                                          int percentage)
                                                                                                                                   throws java.io.IOException,
                                                                                                                                          java.lang.InterruptedException

This classifies all the interactions into those with the same sequence ie two domain interactions have the same pairwise sequences A->A' is same sequence and B->B' is same sequence - not is one domain interaction a homodimer.

Parameters:

map -

counter -

start -

end -

percentage -

Returns:

Throws:

java.io.IOException

java.lang.InterruptedException

isSequenceLevelHomodimer

public static boolean isSequenceLevelHomodimer(java.util.Collection<DomainInteraction> domainInteractions,
                                               int percentage)
                                        throws java.io.IOException,
                                               java.lang.InterruptedException

Throws:

java.io.IOException

java.lang.InterruptedException

getSequenceSimilarInteractions

public static java.util.List<java.util.List<DomainInteraction>> getSequenceSimilarInteractions(java.util.Collection<DomainInteraction> familyClassifiedInteractions,
                                                                                               int percentage)
                                                                                        throws java.io.IOException,
                                                                                               java.lang.InterruptedException

Throws:

java.io.IOException

java.lang.InterruptedException

classifyInteractionsIntoThoseWithSameSequence

public static void classifyInteractionsIntoThoseWithSameSequence(java.util.List<java.util.List<DomainInteraction>> sameList,
                                                                 java.util.List<DomainInteraction> startingList,
                                                                 int percentage)
                                                          throws java.io.IOException,
                                                                 java.lang.InterruptedException

Throws:

java.io.IOException

java.lang.InterruptedException

domainsHaveSameSequence

public static boolean domainsHaveSameSequence(DomainInteraction di0,
                                              DomainInteraction di1,
                                              int percentage)
                                       throws java.io.IOException,
                                              java.lang.InterruptedException

Throws:

java.io.IOException

java.lang.InterruptedException