Package org.biojava.nbio.core.sequence.storage

Class SequenceAsStringHelper<C extends Compound>

java.lang.Object

org.biojava.nbio.core.sequence.storage.SequenceAsStringHelper<C>

public class SequenceAsStringHelper<C extends Compound>
extends Object

This is a common method that can be used across multiple storage/proxy implementations to handle Negative strand and other interesting elements of sequence data.

Author:

Scooter Willis

Constructor Summary

Constructors

Constructor	Description
SequenceAsStringHelper()

Method Summary

Modifier and Type	Method	Description
String	getSequenceAsString(List<C> parsedCompounds, CompoundSet<C> compoundSet, Integer bioBegin, Integer bioEnd, Strand strand)

Methods inherited from class java.lang.Object

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

Constructor Detail

SequenceAsStringHelper

public SequenceAsStringHelper()

Method Detail

getSequenceAsString

public String getSequenceAsString(List<C> parsedCompounds,
                                  CompoundSet<C> compoundSet,
                                  Integer bioBegin,
                                  Integer bioEnd,
                                  Strand strand)

Parameters:

parsedCompounds -

compoundSet -

bioBegin -

bioEnd -

strand -

Returns: