info.bioinfweb.commons.bio

Class ConsensusSequenceCreator

java.lang.Object

info.bioinfweb.commons.bio.ConsensusSequenceCreator

public class ConsensusSequenceCreator
extends java.lang.Object

Method Summary

Modifier and Type	Method and Description
static ConsensusSequenceCreator	getInstance()
org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound>	majorityRuleConsensus(java.util.List<? extends org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound>> sequences)
org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound>	majorityRuleConsensus(org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound>[] sequences) Constructs a majority rule consensus sequence.
java.lang.String	majorityRuleConsensusAsString(java.util.List<? extends org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound>> sequences)
java.lang.String	majorityRuleConsensusAsString(org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound>[] sequences) Constructs a majority rule consensus sequence.

Methods inherited from class java.lang.Object

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

Method Detail

getInstance

public static ConsensusSequenceCreator getInstance()

majorityRuleConsensusAsString

public java.lang.String majorityRuleConsensusAsString(java.util.List<? extends org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound>> sequences)

majorityRuleConsensusAsString

public java.lang.String majorityRuleConsensusAsString(org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound>[] sequences)

Constructs a majority rule consensus sequence. The returned sequence always contains T instead of U, even if RNA sequences have been specified.

Parameters:

sequences - a set of sequences with equal length

Returns:

the consensus sequence

majorityRuleConsensus

public org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound> majorityRuleConsensus(org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound>[] sequences)

Constructs a majority rule consensus sequence.

Parameters:

sequences - a set of sequences with equal length

Returns:

the consensus sequence

majorityRuleConsensus

public org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound> majorityRuleConsensus(java.util.List<? extends org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound>> sequences)