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

Class ReplaceAbstractSequenceView

java.lang.Object

org.biojava3.core.sequence.template.SequenceProxyView<org.biojava3.core.sequence.compound.NucleotideCompound>

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

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

All Implemented Interfaces:

CountableSequenceView, java.lang.Iterable<org.biojava3.core.sequence.compound.NucleotideCompound>, org.biojava3.core.sequence.template.Accessioned, org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound>, org.biojava3.core.sequence.template.SequenceView<org.biojava3.core.sequence.compound.NucleotideCompound>

public class ReplaceAbstractSequenceView
extends ReplaceNucleotideSequenceView

Field Summary

Fields inherited from class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ReplaceNucleotideSequenceView

AMBIGUITY_DNA_TO_N_RNA_MAP, AMBIGUITY_RNA_TO_N_DNA_MAP, AMBIGUITY_TO_N_MAP, AMBIGUITY_UNKNOWN_DNA_TO_N_RNA_MAP, AMBIGUITY_UNKNOWN_RNA_TO_N_DNA_MAP, DNA_TO_RNA_MAP, RNA_TO_DNA_MAP, UNKNOWN_DNA_TO_N_RNA_MAP, UNKNOWN_RNA_TO_N_DNA_MAP

Constructor Summary

Constructors

Constructor and Description
ReplaceAbstractSequenceView(org.biojava3.core.sequence.template.AbstractSequence<org.biojava3.core.sequence.compound.NucleotideCompound> sequence, java.util.Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> replacementMap)

Method Summary

Modifier and Type	Method and Description
java.lang.String	getOriginalHeader()

Methods inherited from class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ReplaceNucleotideSequenceView

countChangedCompounds, getCompoundAt

Methods inherited from class org.biojava3.core.sequence.template.SequenceProxyView

countCompounds, getAccession, getAsList, getBioEnd, getBioStart, getCompoundSet, getIndexOf, getInverse, getLastIndexOf, getLength, getSequenceAsString, getSubSequence, getViewedSequence, iterator, setBioEnd, setBioStart

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biojava3.core.sequence.template.SequenceView

getBioEnd, getBioStart, getViewedSequence

Methods inherited from interface org.biojava3.core.sequence.template.Sequence

countCompounds, getAsList, getCompoundSet, getIndexOf, getInverse, getLastIndexOf, getLength, getSequenceAsString, getSubSequence

Methods inherited from interface java.lang.Iterable

forEach, iterator, spliterator

Methods inherited from interface org.biojava3.core.sequence.template.Accessioned

getAccession

Constructor Detail

ReplaceAbstractSequenceView

public ReplaceAbstractSequenceView(org.biojava3.core.sequence.template.AbstractSequence<org.biojava3.core.sequence.compound.NucleotideCompound> sequence,
                                   java.util.Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> replacementMap)

Method Detail

getOriginalHeader

public java.lang.String getOriginalHeader()