org.biojava.nbio.core.sequence.template

Class SequenceProxyView<C extends Compound>

java.lang.Object

org.biojava.nbio.core.sequence.template.SequenceProxyView<C>

All Implemented Interfaces:

Iterable<C>, Accessioned, Sequence<C>, SequenceView<C>

Direct Known Subclasses:

ComplementSequenceView, ReversedSequenceView, RnaSequenceView

public class SequenceProxyView<C extends Compound>
extends Object
implements SequenceView<C>

Constructor Summary

Constructors

Constructor and Description
SequenceProxyView()
SequenceProxyView(Sequence<C> sequence)
SequenceProxyView(Sequence<C> sequence, Integer bioStart, Integer bioEnd) Main constructor for working with SequenceProxyViews

Method Summary

Methods

Modifier and Type	Method and Description
int	countCompounds(C... compounds) Returns the number of times we found a compound in the Sequence
AccessionID	getAccession() Returns the AccessionID this location is currently bound with
List<C>	getAsList() Returns the Sequence as a List of compounds
Integer	getBioEnd() 1-indexed, inclusive.
Integer	getBioStart() 1-indexed, inclusive.
C	getCompoundAt(int position) Returns the Compound at the given biological index
CompoundSet<C>	getCompoundSet() Gets the compound set used to back this Sequence
int	getIndexOf(C compound) Scans through the Sequence looking for the first occurrence of the given compound
SequenceView<C>	getInverse() Does the right thing to get the inverse of the current Sequence.
int	getLastIndexOf(C compound) Scans through the Sequence looking for the last occurrence of the given compound
int	getLength() Returns the length of the Sequence
String	getSequenceAsString() Returns the String representation of the Sequence
SequenceView<C>	getSubSequence(Integer bioStart, Integer bioEnd) Returns a portion of the sequence from the different positions.
Sequence<C>	getViewedSequence()
Iterator<C>	iterator()
void	setBioEnd(Integer bioEnd)
void	setBioStart(Integer bioStart)

Methods inherited from class java.lang.Object

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

Constructor Detail

SequenceProxyView

public SequenceProxyView()

SequenceProxyView

public SequenceProxyView(Sequence<C> sequence)

SequenceProxyView

public SequenceProxyView(Sequence<C> sequence,
                 Integer bioStart,
                 Integer bioEnd)

Main constructor for working with SequenceProxyViews

Parameters:

sequence - Sequence to proxy

bioStart - Start; cannot be less than 1

bioEnd - End; cannot be greater than the sequence length

Method Detail

getViewedSequence

public Sequence<C> getViewedSequence()

Specified by:

getViewedSequence in interface SequenceView<C extends Compound>

getSequenceAsString

public String getSequenceAsString()

Description copied from interface: Sequence

Returns the String representation of the Sequence

Specified by:

getSequenceAsString in interface Sequence<C extends Compound>

getAsList

public List<C> getAsList()

Description copied from interface: Sequence

Returns the Sequence as a List of compounds

Specified by:

getAsList in interface Sequence<C extends Compound>

getCompoundAt

public C getCompoundAt(int position)

Description copied from interface: Sequence

Returns the Compound at the given biological index

Specified by:

getCompoundAt in interface Sequence<C extends Compound>

Parameters:

position - Biological index (1 to n)

Returns:

Compound at the specified position

getIndexOf

public int getIndexOf(C compound)

Description copied from interface: Sequence

Scans through the Sequence looking for the first occurrence of the given compound

Specified by:

getIndexOf in interface Sequence<C extends Compound>

Parameters:

compound - Compounds to look for

Returns:

Index of the first position of the compound in the sequence (1 to n)

getLastIndexOf

public int getLastIndexOf(C compound)

Description copied from interface: Sequence

Scans through the Sequence looking for the last occurrence of the given compound

Specified by:

getLastIndexOf in interface Sequence<C extends Compound>

Parameters:

compound - Compounds to look for

Returns:

Index of the last position of the compound in the sequence (1 to n)

getLength

public int getLength()

Description copied from interface: Sequence

Returns the length of the Sequence

Specified by:

getLength in interface Sequence<C extends Compound>

getCompoundSet

public CompoundSet<C> getCompoundSet()

Description copied from interface: Sequence

Gets the compound set used to back this Sequence

Specified by:

getCompoundSet in interface Sequence<C extends Compound>

getSubSequence

public SequenceView<C> getSubSequence(Integer bioStart,
                             Integer bioEnd)

Description copied from interface: Sequence

Returns a portion of the sequence from the different positions. This is indexed from 1

Specified by:

getSubSequence in interface Sequence<C extends Compound>

Parameters:

bioStart - Biological index start; must be greater than 0

bioEnd - Biological end; must be less than length + 1

Returns:

A SequenceView of the offset

iterator

public Iterator<C> iterator()

Specified by:

iterator in interface Iterable<C extends Compound>

getAccession

public AccessionID getAccession()

Description copied from interface: Accessioned

Returns the AccessionID this location is currently bound with

Specified by:

getAccession in interface Accessioned

getBioStart

public Integer getBioStart()

Description copied from interface: SequenceView

1-indexed, inclusive.

Specified by:

getBioStart in interface SequenceView<C extends Compound>

Returns:

the bioStart

setBioStart

public void setBioStart(Integer bioStart)

Parameters:

bioStart - the bioStart to set

getBioEnd

public Integer getBioEnd()

Description copied from interface: SequenceView

1-indexed, inclusive.

Specified by:

getBioEnd in interface SequenceView<C extends Compound>

Returns:

the bioEnd

setBioEnd

public void setBioEnd(Integer bioEnd)

Parameters:

bioEnd - the bioEnd to set

countCompounds

public int countCompounds(C... compounds)

Description copied from interface: Sequence

Returns the number of times we found a compound in the Sequence

Specified by:

countCompounds in interface Sequence<C extends Compound>

Parameters:

compounds - Vargs of the compounds to count

Returns:

Number of times a compound was found

getInverse

public SequenceView<C> getInverse()

Description copied from interface: Sequence

Does the right thing to get the inverse of the current Sequence. This means either reversing the Sequence and optionally complementing the Sequence.

Specified by:

getInverse in interface Sequence<C extends Compound>