org.biojava.nbio.core.sequence.loader

Class StringProxySequenceReader<C extends Compound>

java.lang.Object

org.biojava.nbio.core.sequence.loader.StringProxySequenceReader<C>

Type Parameters:

C -

All Implemented Interfaces:

Iterable<C>, Accessioned, ProxySequenceReader<C>, Sequence<C>, SequenceReader<C>

Direct Known Subclasses:

GenbankProxySequenceReader

public class StringProxySequenceReader<C extends Compound>
extends Object
implements ProxySequenceReader<C>

An example of a ProxySequenceReader that is created from a String. Used for testing

Author:

Scooter Willis

Constructor Summary

Constructors

Constructor and Description
StringProxySequenceReader()
StringProxySequenceReader(String sequence, CompoundSet<C> compoundSet)

Method Summary

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
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
String	getSequenceAsString(Integer bioBegin, Integer bioEnd, Strand strand)
SequenceView<C>	getSubSequence(Integer bioBegin, Integer bioEnd) Returns a portion of the sequence from the different positions.
Iterator<C>	iterator()
void	setCompoundSet(CompoundSet<C> compoundSet)
void	setContents(String sequence)
void	setContents(String sequence, ArrayList features)
String	toString()

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

StringProxySequenceReader

public StringProxySequenceReader()

StringProxySequenceReader

public StringProxySequenceReader(String sequence,
                                 CompoundSet<C> compoundSet)
                          throws CompoundNotFoundException

Throws:

CompoundNotFoundException

Method Detail

setCompoundSet

public void setCompoundSet(CompoundSet<C> compoundSet)

Specified by:

setCompoundSet in interface SequenceReader<C extends Compound>

setContents

public void setContents(String sequence)
                 throws CompoundNotFoundException

Specified by:

setContents in interface SequenceReader<C extends Compound>

Throws:

CompoundNotFoundException

setContents

public void setContents(String sequence,
                        ArrayList features)
                 throws CompoundNotFoundException

Throws:

CompoundNotFoundException

getLength

public int getLength()

Description copied from interface: Sequence

Returns the length of the Sequence

Specified by:

getLength 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)

toString

public String toString()

Overrides:

toString in class Object

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>

getSequenceAsString

public String getSequenceAsString(Integer bioBegin,
                                  Integer bioEnd,
                                  Strand strand)

getSubSequence

public SequenceView<C> getSubSequence(Integer bioBegin,
                                      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:

bioBegin - 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>

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>

getAccession

public AccessionID getAccession()

Description copied from interface: Accessioned

Returns the AccessionID this location is currently bound with

Specified by:

getAccession in interface Accessioned

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>