Package org.biojava.nbio.core.sequence.loader

Class SequenceFileProxyLoader<C extends Compound>

java.lang.Object

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

Type Parameters:

C - the compound type

All Implemented Interfaces:

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

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

This class represents the storage container of a sequence stored in a fasta file where the initial parsing of the file we store the offset and length of the sequence. When a call is made to any method that needs sequence data then the file will be opened and the sequence loaded. This class could be improved by using the hints or a some algorithm that indicates the sequence data once loaded should stay loaded. Could keep track of the last time sequence data was loaded and then after X amount of time clear the contents to free up memory.

Author:

Scooter Willis

Constructor Summary

Constructors

Constructor	Description
SequenceFileProxyLoader(File file, SequenceParserInterface sequenceParser, long sequenceStartIndex, int sequenceLength, CompoundSet<C> compoundSet)

Method Summary

Modifier and Type	Method	Description
int	countCompounds(C... compounds)	Returns the number of times we found a compound in the Sequence
boolean	equals(Object o)
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.
int	hashCode()
Iterator<C>	iterator()
void	setCompoundSet(CompoundSet<C> compoundSet)
void	setContents(String sequence)
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Details

SequenceFileProxyLoader

public SequenceFileProxyLoader(File file,
 SequenceParserInterface sequenceParser,
 long sequenceStartIndex,
 int sequenceLength,
 CompoundSet<C> compoundSet)
                        throws IOException,
CompoundNotFoundException

Parameters:

file - The file where the sequence will be found

sequenceParser - The parser to use to load the sequence

sequenceStartIndex - The file offset to the start of the sequence

sequenceLength - The length of the sequence

compoundSet -

Throws:

IOException - if problems occur while reading the file

CompoundNotFoundException - if a compound in the sequence can't be found in the given compoundSet

Method Details

setCompoundSet

public void setCompoundSet(CompoundSet<C> compoundSet)

Specified by:

setCompoundSet in interface SequenceReader<C extends Compound>

Parameters:

compoundSet -

setContents

public void setContents(String sequence)
                 throws CompoundNotFoundException

Specified by:

setContents in interface SequenceReader<C extends Compound>

Parameters:

sequence -

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>

Returns:

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 -

Returns:

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 -

Returns:

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 -

Returns:

toString

public String toString()

Overrides:

toString in class Object

Returns:

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>

Returns:

getSequenceAsString

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

Parameters:

bioBegin -

bioEnd -

strand -

Returns:

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>

Returns:

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

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 -

bioEnd -

Returns:

iterator

public Iterator<C> iterator()

Specified by:

iterator in interface Iterable<C extends Compound>

Returns:

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>

Returns:

getAccession

public AccessionID getAccession()

Description copied from interface: Accessioned

Returns the AccessionID this location is currently bound with

Specified by:

getAccession in interface Accessioned

Returns:

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 -

Returns:

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>

Returns: