info.bioinfweb.libralign.model.adapters

Class SingleBioJava3SequenceAdapter<T,C extends org.biojava3.core.sequence.template.Compound>

java.lang.Object

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

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

info.bioinfweb.libralign.model.adapters.SingleBioJava3SequenceAdapter<T,C>

Type Parameters:

T - the token type of the underlying data source

C - the compound type of the provided BioJava sequences

All Implemented Interfaces:

SingleSequenceDataAdapter<T>, BasicAlignmentModelView<T>, java.lang.Iterable<C>, org.biojava3.core.sequence.template.Accessioned, org.biojava3.core.sequence.template.Sequence<C>

public class SingleBioJava3SequenceAdapter<T,C extends org.biojava3.core.sequence.template.Compound>
extends AbstractSingleSequenceDataAdapter<T>
implements org.biojava3.core.sequence.template.Sequence<C>

Abstract base class for all implementations of SingleSequenceDataAdapter that allow to view one sequence of a AlignmentModel as a BioJava Sequence object.

Note that the underlying sequence data provider is directly used to that all changes in that provider are also reflected by the instance of this class.

Since:

0.1.0

Author:

Ben Stöver

Module:

info.bioinfweb.libralign.biojava3

Constructor Summary

Constructors

Constructor and Description
SingleBioJava3SequenceAdapter(AlignmentModel<T> underlyingProvider, java.lang.String sequenceID, org.biojava3.core.sequence.template.CompoundSet<C> compoundSet) Creates a new instance of this class that does not allow unknown compounds.
SingleBioJava3SequenceAdapter(AlignmentModel<T> underlyingProvider, java.lang.String sequenceID, org.biojava3.core.sequence.template.CompoundSet<C> compoundSet, C unknownCompound) Creates a new instance of this class allowing unknown compounds.
SingleBioJava3SequenceAdapter(AlignmentModel<T> underlyingProvider, java.lang.String sequenceID, int offset, int length, org.biojava3.core.sequence.template.CompoundSet<C> compoundSet) Creates a new instance of this class that does not allow unknown compounds.
SingleBioJava3SequenceAdapter(AlignmentModel<T> underlyingProvider, java.lang.String sequenceID, int offset, int length, org.biojava3.core.sequence.template.CompoundSet<C> compoundSet, C unknownCompound) Creates a new instance of this class allowing unknown compounds.

Method Summary

Modifier and Type	Method and Description
int	countCompounds(C... compounds)
org.biojava3.core.sequence.AccessionID	getAccession() This method always returns null since sequences stored in instances of AlignmentModel do not store an associated instance of AccessionID.
java.util.List<C>	getAsList()
C	getCompoundAt(int index)
org.biojava3.core.sequence.template.CompoundSet<C>	getCompoundSet()
int	getIndexOf(C compound)
org.biojava3.core.sequence.template.SequenceView<C>	getInverse()
int	getLastIndexOf(C compound)
java.lang.String	getSequenceAsString()
org.biojava3.core.sequence.template.SequenceView<C>	getSubSequence(java.lang.Integer start, java.lang.Integer end)
C	getUnknownCompound() Returns the compound that will be inserted into the BioJava sequence if no according compound to the token in the underlying data source can be found in the specified compound set.
boolean	isAllowUnkownCompounds()
java.util.Iterator<C>	iterator()

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

getLength, getOffset, getSequenceID, setLength, setOffset, setSequenceID

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 org.biojava3.core.sequence.template.Sequence

getLength

Methods inherited from interface java.lang.Iterable

forEach, spliterator

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

getUnderlyingModel

Constructor Detail

SingleBioJava3SequenceAdapter

public SingleBioJava3SequenceAdapter(AlignmentModel<T> underlyingProvider,
                                     java.lang.String sequenceID,
                                     int offset,
                                     int length,
                                     org.biojava3.core.sequence.template.CompoundSet<C> compoundSet)

Creates a new instance of this class that does not allow unknown compounds.

Parameters:

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

sequenceID - the ID used in provider 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

compoundSet - the compound set to be used for the translation

SingleBioJava3SequenceAdapter

public SingleBioJava3SequenceAdapter(AlignmentModel<T> underlyingProvider,
                                     java.lang.String sequenceID,
                                     int offset,
                                     int length,
                                     org.biojava3.core.sequence.template.CompoundSet<C> compoundSet,
                                     C unknownCompound)

Creates a new instance of this class allowing unknown compounds.

Parameters:

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

sequenceID - the ID used in provider 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

compoundSet - the compound set to be used for the translation

unknownCompound - the compound that will be inserted into the BioJava sequence if no according compound to the token in the underlying data source can be found in compoundSet

SingleBioJava3SequenceAdapter

public SingleBioJava3SequenceAdapter(AlignmentModel<T> underlyingProvider,
                                     java.lang.String sequenceID,
                                     org.biojava3.core.sequence.template.CompoundSet<C> compoundSet)

Creates a new instance of this class that does not allow unknown compounds.

Parameters:

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

sequenceID - the ID used in provider of the sequence to be viewed

compoundSet - the compound set to be used for the translation

SingleBioJava3SequenceAdapter

public SingleBioJava3SequenceAdapter(AlignmentModel<T> underlyingProvider,
                                     java.lang.String sequenceID,
                                     org.biojava3.core.sequence.template.CompoundSet<C> compoundSet,
                                     C unknownCompound)

Creates a new instance of this class allowing unknown compounds.

Parameters:

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

sequenceID - the ID used in provider of the sequence to be viewed

compoundSet - the compound set to be used for the translation

unknownCompound - the compound that will be inserted into the BioJava sequence if no according compound to the token in the underlying data source can be found in compoundSet

Method Detail

isAllowUnkownCompounds

public boolean isAllowUnkownCompounds()

getUnknownCompound

public C getUnknownCompound()

Returns the compound that will be inserted into the BioJava sequence if no according compound to the token in the underlying data source can be found in the specified compound set.

Returns:

the unknown compound that was specified in the constructor

getCompoundAt

public C getCompoundAt(int index)

Specified by:

getCompoundAt in interface org.biojava3.core.sequence.template.Sequence<C extends org.biojava3.core.sequence.template.Compound>

Parameters:

index -

Returns:

Throws:

InvalidUnderlyingTokenException

getCompoundSet

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

Specified by:

getCompoundSet in interface org.biojava3.core.sequence.template.Sequence<C extends org.biojava3.core.sequence.template.Compound>

iterator

public java.util.Iterator<C> iterator()

Specified by:

iterator in interface java.lang.Iterable<C extends org.biojava3.core.sequence.template.Compound>

getAccession

public org.biojava3.core.sequence.AccessionID getAccession()

This method always returns null since sequences stored in instances of AlignmentModel do not store an associated instance of AccessionID.

Specified by:

getAccession in interface org.biojava3.core.sequence.template.Accessioned

See Also:

Accessioned.getAccession()

countCompounds

public int countCompounds(C... compounds)

Specified by:

countCompounds in interface org.biojava3.core.sequence.template.Sequence<C extends org.biojava3.core.sequence.template.Compound>

getAsList

public java.util.List<C> getAsList()

Specified by:

getAsList in interface org.biojava3.core.sequence.template.Sequence<C extends org.biojava3.core.sequence.template.Compound>

getIndexOf

public int getIndexOf(C compound)

Specified by:

getIndexOf in interface org.biojava3.core.sequence.template.Sequence<C extends org.biojava3.core.sequence.template.Compound>

getInverse

public org.biojava3.core.sequence.template.SequenceView<C> getInverse()

Specified by:

getInverse in interface org.biojava3.core.sequence.template.Sequence<C extends org.biojava3.core.sequence.template.Compound>

getLastIndexOf

public int getLastIndexOf(C compound)

Specified by:

getLastIndexOf in interface org.biojava3.core.sequence.template.Sequence<C extends org.biojava3.core.sequence.template.Compound>

getSequenceAsString

public java.lang.String getSequenceAsString()

Specified by:

getSequenceAsString in interface org.biojava3.core.sequence.template.Sequence<C extends org.biojava3.core.sequence.template.Compound>

getSubSequence

public org.biojava3.core.sequence.template.SequenceView<C> getSubSequence(java.lang.Integer start,
                                                                          java.lang.Integer end)

Specified by:

getSubSequence in interface org.biojava3.core.sequence.template.Sequence<C extends org.biojava3.core.sequence.template.Compound>