info.bioinfweb.libralign.model.adapters

Class BioJava3SequenceAdapter<T,C extends org.biojava3.core.sequence.template.Compound>

java.lang.Object

info.bioinfweb.libralign.model.adapters.AbstractBasicAlignmentModelView<T>

info.bioinfweb.libralign.model.adapters.BioJava3SequenceAdapter<T,C>

Type Parameters:

T - the token type used by the underlying provider

C - the compound class to be used in the returned sequences

All Implemented Interfaces:

SequenceDataAdapter<SingleBioJava3SequenceAdapter<T,C>,T>, BasicAlignmentModelView<T>, SequenceAccess<SingleBioJava3SequenceAdapter<T,C>>

public class BioJava3SequenceAdapter<T,C extends org.biojava3.core.sequence.template.Compound>
extends AbstractBasicAlignmentModelView<T>
implements SequenceDataAdapter<SingleBioJava3SequenceAdapter<T,C>,T>

Adapter class that allows to access the contents of an implementation of AlignmentModel as a set of BioJava Sequence objects.

Since:

0.1.0

Author:

Ben Stöver

Module:

info.bioinfweb.libralign.biojava3

Constructor Summary

Constructors

Constructor and Description
BioJava3SequenceAdapter(AlignmentModel<T> underlyingProvider, org.biojava3.core.sequence.template.CompoundSet<C> compoundSet) Creates a new instance of this class.

Method Summary

Modifier and Type	Method and Description
org.biojava3.core.sequence.template.CompoundSet<C>	getCompoundSet() Returns the compound set to be used for the translation.
SingleBioJava3SequenceAdapter<T,C>	getSequence(java.lang.String sequenceID) Returns an implementation of Sequence that acts as a view to the sequence with the specified ID in the underlying data source.
SingleBioJava3SequenceAdapter<T,C>	getSubSequence(java.lang.String sequenceID, int offset, int length) Returns an implementation of Sequence that acts as a view to a subsequence of the sequence with the specified ID in the underlying data source.
boolean	returnsCopies() Returns false since this class always returns views of the underlying data source.
org.biojava3.core.sequence.template.LightweightProfile<org.biojava3.core.sequence.template.Sequence<C>,C>	toLightweightProfile() Returns a BioJava alignment that contains the views of all sequences contained in the underlying data source in the order they are stored there.
org.biojava3.core.sequence.template.LightweightProfile<org.biojava3.core.sequence.template.Sequence<C>,C>	toLightweightProfile(SequenceOrder order) Returns a BioJava alignment that contains the views of all sequences contained in the underlying data source in the order specified in the order object.

Methods inherited from class info.bioinfweb.libralign.model.adapters.AbstractBasicAlignmentModelView

getUnderlyingModel, setUnderlyingModel

Methods inherited from class java.lang.Object

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

Methods inherited from interface info.bioinfweb.libralign.model.BasicAlignmentModelView

getUnderlyingModel

Constructor Detail

BioJava3SequenceAdapter

public BioJava3SequenceAdapter(AlignmentModel<T> underlyingProvider,
                               org.biojava3.core.sequence.template.CompoundSet<C> compoundSet)

Creates a new instance of this class.

Parameters:

provider - the sequence data provider that contains the sequences to be viewed

compoundSet - the compound set to be used for the translation

Method Detail

getCompoundSet

public org.biojava3.core.sequence.template.CompoundSet<C> getCompoundSet()

Returns the compound set to be used for the translation.

Returns:

the compound set that was specified in the constructor

getSequence

public SingleBioJava3SequenceAdapter<T,C> getSequence(java.lang.String sequenceID)

Returns an implementation of Sequence that acts as a view to the sequence with the specified ID in the underlying data source.

Specified by:

getSequence in interface SequenceAccess<SingleBioJava3SequenceAdapter<T,C extends org.biojava3.core.sequence.template.Compound>>

Parameters:

sequenceID - the ID of the sequence to be viewed

Returns:

a sequence as an Sequence object

getSubSequence

public SingleBioJava3SequenceAdapter<T,C> getSubSequence(java.lang.String sequenceID,
                                                         int offset,
                                                         int length)

Returns an implementation of Sequence that acts as a view to a subsequence of the sequence with the specified ID in the underlying data source.

Specified by:

getSubSequence in interface SequenceDataAdapter<SingleBioJava3SequenceAdapter<T,C extends org.biojava3.core.sequence.template.Compound>,T>

Parameters:

sequenceID - the ID of the sequence to be viewed

offset - the start index of the subsequence to be viewed (The first token has the index 0.)

length - the length of the subsequence to be viewed

Returns:

a subsequence as an Sequence object

toLightweightProfile

public org.biojava3.core.sequence.template.LightweightProfile<org.biojava3.core.sequence.template.Sequence<C>,C> toLightweightProfile()

Returns a BioJava alignment that contains the views of all sequences contained in the underlying data source in the order they are stored there.

Returns:

an instance of MultipleSequenceAlignment (Note that the implementation type of LightweightProfile might change in future releases of LibrAlign.)

toLightweightProfile

public org.biojava3.core.sequence.template.LightweightProfile<org.biojava3.core.sequence.template.Sequence<C>,C> toLightweightProfile(SequenceOrder order)

Returns a BioJava alignment that contains the views of all sequences contained in the underlying data source in the order specified in the order object. This method can be used to obtain an BioJava alignment with the same order as an AlignmentArea area displaying these sequences.

Parameters:

order - the object specifying the order of the sequences in the returned alignment

Returns:

an instance of MultipleSequenceAlignment (Note that the implementation type of LightweightProfile might change in future releases of LibrAlign.)

returnsCopies

public boolean returnsCopies()

Returns false since this class always returns views of the underlying data source.

Specified by:

returnsCopies in interface SequenceDataAdapter<SingleBioJava3SequenceAdapter<T,C extends org.biojava3.core.sequence.template.Compound>,T>

Returns:

false