com.hfg.bio.seq

Class SeqUtil

java.lang.Object

com.hfg.bio.seq.SeqUtil

public class SeqUtil
extends Object

Utility class of generic sequence functions.

Constructor Summary

Constructors

Constructor and Description
SeqUtil()

Method Summary

Modifier and Type	Method and Description
static SeqLocation	flipStrandSeqLocation(SeqLocation inSeqLoc, int inNucleotideSeqLength) Creates a new SeqLocation that is relative to the opposite strand.
static String	getReverseComplementSequence(String inNucleicAcidSeq)
static BioSequenceType	guessBioSequenceType(String inSequence) Guesses the BioSequenceType for the specified sequence.
static <T extends BioSequence> Collection<T>	unique(Collection<T> inSequences) Retains only a single copy of each distinct sequence.

Methods inherited from class java.lang.Object

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

Constructor Detail

SeqUtil

public SeqUtil()

Method Detail

unique

public static <T extends BioSequence> Collection<T> unique(Collection<T> inSequences)

Retains only a single copy of each distinct sequence.

Type Parameters:

T - BioSequence-implementing class

Parameters:

inSequences - the collection of (potentially redundant) input sequences

Returns:

the non-redundant collection of sequences

guessBioSequenceType

public static BioSequenceType guessBioSequenceType(String inSequence)

Guesses the BioSequenceType for the specified sequence. If the sequence is greater than 80% ATUGCN, it will be called as NUCLEIC_ACID. Otherwise it will be called as PROTEIN.

Parameters:

inSequence - the sequence to guess the sequence type from

Returns:

the BioSequenceType of the input sequence

getReverseComplementSequence

public static String getReverseComplementSequence(String inNucleicAcidSeq)

flipStrandSeqLocation

public static SeqLocation flipStrandSeqLocation(SeqLocation inSeqLoc,
                                                int inNucleotideSeqLength)

Creates a new SeqLocation that is relative to the opposite strand. Ex: [2, 6] on the reverse strand of a nucleotide sequence of length 10, would be converted to a forward strand relative location of [9, 5].

Parameters:

inSeqLoc - the initial sequence location

inNucleotideSeqLength - the length of the nucleotide sequence containing the location

Returns:

a SeqLocation relative to the opposite strand