info.bioinfweb.commons.bio.biojava3.core.sequence

Class SequenceCompareUtils

java.lang.Object

info.bioinfweb.commons.bio.biojava3.core.sequence.SequenceCompareUtils

public class SequenceCompareUtils
extends java.lang.Object

Helper class that allows to compare sequences by taking ambiguity codes into account or not.

Author:

Ben Stöver

Constructor Summary

Constructors

Constructor and Description
SequenceCompareUtils()

Method Summary

Modifier and Type	Method and Description
static <C extends org.biojava3.core.sequence.compound.NucleotideCompound,S extends org.biojava3.core.sequence.template.Sequence<C>> boolean	nucleotideSequencesEquivalent(S sequence1, S sequence2) The two sequences are considered equivalent of the symbols on each position match.
static boolean	sequencesEqual(org.biojava3.core.sequence.template.Sequence<? extends org.biojava3.core.sequence.template.Compound> sequence1, org.biojava3.core.sequence.template.Sequence<? extends org.biojava3.core.sequence.template.Compound> sequence2) Tests if the two symbols at each according position of the two sequences are exactly equal.
static <C extends org.biojava3.core.sequence.template.Compound,S extends org.biojava3.core.sequence.template.Sequence<C>> boolean	sequencesEquivalent(org.biojava3.core.sequence.template.CompoundSet<? super C> set, S sequence1, S sequence2) Uses the AbstractCompoundSet.compoundsEquivalent(Compound, Compound) method of the specified compound set to check if the values at each position of the two sequences are equal.

Methods inherited from class java.lang.Object

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

Constructor Detail

SequenceCompareUtils

public SequenceCompareUtils()

Method Detail

sequencesEqual

public static boolean sequencesEqual(org.biojava3.core.sequence.template.Sequence<? extends org.biojava3.core.sequence.template.Compound> sequence1,
                                     org.biojava3.core.sequence.template.Sequence<? extends org.biojava3.core.sequence.template.Compound> sequence2)

Tests if the two symbols at each according position of the two sequences are exactly equal. (If ambiguity codes are contained they have to be identical at the according positions. Example: N == N, but N != B) T and U are not considered equal.

Parameters:

sequence1 -

sequence2 -

Returns:

sequencesEquivalent

public static <C extends org.biojava3.core.sequence.template.Compound,S extends org.biojava3.core.sequence.template.Sequence<C>> boolean sequencesEquivalent(org.biojava3.core.sequence.template.CompoundSet<? super C> set,
                                                                                                                                                             S sequence1,
                                                                                                                                                             S sequence2)

Uses the AbstractCompoundSet.compoundsEquivalent(Compound, Compound) method of the specified compound set to check if the values at each position of the two sequences are equal.

Parameters:

set -

sequence1 -

sequence2 -

Returns:

nucleotideSequencesEquivalent

public static <C extends org.biojava3.core.sequence.compound.NucleotideCompound,S extends org.biojava3.core.sequence.template.Sequence<C>> boolean nucleotideSequencesEquivalent(S sequence1,
                                                                                                                                                                                 S sequence2)

The two sequences are considered equivalent of the symbols on each position match. If ambiguity codes are contained they are considered equal if one set is completely contained in the other. T and U are considered equivalent. This method uses AlignmentAmbiguityNucleotideCompoundSet internally.

Parameters:

sequence1 -

sequence2 -

Returns: