com.hfg.bio.seq.format.feature.genbank

Class GenBankFeatureLocation

java.lang.Object

com.hfg.bio.seq.format.feature.genbank.GenBankFeatureLocation

All Implemented Interfaces:

SeqFeatureLocation, Comparable

Direct Known Subclasses:

GenomicLocation

public class GenBankFeatureLocation
extends Object
implements SeqFeatureLocation

GenBank feature location. Not all location expression types are currently supported for methods like eval().

See http://www.insdc.org/documents/feature-table#3.4.3

Constructor Summary

Constructors

Constructor and Description
GenBankFeatureLocation(String inLocationString)

Method Summary

Modifier and Type	Method and Description
void	append(String inAdditionalLocationData)
GenBankFeatureLocation	clone()
int	compareTo(Object inObj2)
boolean	equals(Object inObj2)
String	eval(NucleicAcid inNucleicAcid)
String	eval(String inSequence)
void	extend3Prime(int inAdditionalLength) Extends the last sequence range by the specified number of base pairs.
void	extend5Prime(int inAdditionalLength) Extends the start of the first sequence range by the specified number of base pairs.
Integer	get3Prime()
Integer	get5Prime()
List<SeqLocation>	getIntrons()
Integer	getSeqLength()
int	hashCode()
Long	length()
void	set3Prime(int inValue) Sets the 3' position of the location.
void	set5Prime(int inValue) Sets the 5' position of the location.
GenBankFeatureLocation	setSeqLength(Integer inValue)
Range<Integer>	toIntRange()
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

GenBankFeatureLocation

public GenBankFeatureLocation(String inLocationString)

Method Detail

clone

public GenBankFeatureLocation clone()

Overrides:

clone in class Object

length

public Long length()

setSeqLength

public GenBankFeatureLocation setSeqLength(Integer inValue)

getSeqLength

public Integer getSeqLength()

append

public void append(String inAdditionalLocationData)

Specified by:

append in interface SeqFeatureLocation

extend3Prime

public void extend3Prime(int inAdditionalLength)

Extends the last sequence range by the specified number of base pairs. Supports addition and subtraction for both forward and reverse (ie. complement) location types.

Parameters:

inAdditionalLength - length to extend the last sequence range by

extend5Prime

public void extend5Prime(int inAdditionalLength)

Extends the start of the first sequence range by the specified number of base pairs. Supports addition and subtraction for both forward and reverse (ie. complement) location types.

Parameters:

inAdditionalLength - length to extend the first sequence range by

set5Prime

public void set5Prime(int inValue)

Sets the 5' position of the location. Supports both forward and reverse (ie. complement) location types.

Parameters:

inValue - new 5' position

set3Prime

public void set3Prime(int inValue)

Sets the 3' position of the location. Supports both forward and reverse (ie. complement) location types.

Parameters:

inValue - new 3' position

eval

public String eval(String inSequence)

Specified by:

eval in interface SeqFeatureLocation

eval

public String eval(NucleicAcid inNucleicAcid)

getIntrons

public List<SeqLocation> getIntrons()

toString

public String toString()

Overrides:

toString in class Object

equals

public boolean equals(Object inObj2)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

compareTo

public int compareTo(Object inObj2)

Specified by:

compareTo in interface Comparable

toIntRange

public Range<Integer> toIntRange()

Specified by:

toIntRange in interface SeqFeatureLocation

get5Prime

public Integer get5Prime()

get3Prime

public Integer get3Prime()